September 2004
Volume 45, Issue 9
Free
Biochemistry and Molecular Biology  |   September 2004
Altered Gene Expression in the Eye of a Mouse Model for Batten Disease
Author Affiliations
  • Subrata Chattopadhyay
    From the Center for Aging and Developmental Biology, Aab Institute of Biomedical Sciences; the
  • Evan Kingsley
    From the Center for Aging and Developmental Biology, Aab Institute of Biomedical Sciences; the
  • Andrew Serour
    From the Center for Aging and Developmental Biology, Aab Institute of Biomedical Sciences; the
  • Timothy M. Curran
    From the Center for Aging and Developmental Biology, Aab Institute of Biomedical Sciences; the
  • Andrew I. Brooks
    Departments of Environmental Medicine,
    Center for Functional Genomics, University of Rochester School of Medicine and Dentistry, University of Rochester, Rochester, New York.
  • David A. Pearce
    From the Center for Aging and Developmental Biology, Aab Institute of Biomedical Sciences; the
    Biochemistry and Biophysics, and
    Neurology; and the
Investigative Ophthalmology & Visual Science September 2004, Vol.45, 2893-2905. doi:https://doi.org/10.1167/iovs.04-0143
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      Subrata Chattopadhyay, Evan Kingsley, Andrew Serour, Timothy M. Curran, Andrew I. Brooks, David A. Pearce; Altered Gene Expression in the Eye of a Mouse Model for Batten Disease. Invest. Ophthalmol. Vis. Sci. 2004;45(9):2893-2905. https://doi.org/10.1167/iovs.04-0143.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

purpose. Juvenile neuronal ceroid lipofuscinosis (JNCL or Batten Disease) is one of the most common progressive neurodegenerative disorders of childhood, resulting from autosomal recessive inheritance of mutations in the CLN3 gene. Pathologically, Batten disease is characterized by lysosomal storage of autofluorescent material in all tissue types. Although characterized by seizures, mental retardation, and loss of motor skills, the first presenting symptom of Batten disease is vision loss.

methods. High-density oligonucleotide arrays were used to profile approximately 19,000 mRNAs in the eye of 10-week-old Cln3-knockout and normal mice, and the data were compared with that for the cerebellum in the same model as a means to identify gene expression changes that are specific to the eye.

results. A detailed list was compiled of 285 functionally categorized genes that have altered expression in the eye of Cln3-knockout mice before the appearance of the characteristic lysosomal storage material. Furthermore, 18 genes were identified and 6 validated by semiquantitative RT-PCR that have altered expression in the eye, but not in the cerebellum of Cln3-knockout mice. The genes that have altered expression specific to the eye of the Cln3-knockout mouse may be of importance in understanding the function of CLN3 in different tissues.

conclusions. Downregulation of genes associated with energy production in the mitochondria appears to be specific to the eye. The CLN3 defect may result in altered mitochondrial function in eye but not other tissue. More detailed experimentation is needed to understand the contribution of these changes in expression to disease state, and whether these changes are specific for certain cell types within the eye.

Batten disease or JNCL, is the juvenile form of neuronal ceroid lipofuscinosis (NCL). Batten disease is inherited as an autosomal recessive condition and is the most common progressive neurodegenerative disease of childhood. The disorder is characterized initially by visual deterioration at age 5 to 7 years that ultimately results in blindness. After the loss of vision, other neurologic characteristics are seizures, mental retardation, and loss of motor function. 1 2 Batten disease is always fatal. The CLN3 gene responsible for Batten disease was positionally cloned in 1995, 3 with most individuals with the disease harboring a 1-kb deletion of this gene. The disease is characterized by the accumulation of autofluorescent hydrophobic material in the lysosomes of neurons and other cell types. A predominant component of the lysosomal storage material has been identified as mitochondrial ATP synthase subunit c. 4 5 6 7 One of the paradoxes of Batten disease is that the accumulation of this lysosomal storage material does not apparently lead to disease in non-neuronal cell types. The CLN3 protein has been localized to late endosomes and lysosomes in non-neuronal cell types, and has been shown to co-localize with synaptic vesicle proteins in neuronal cell types 8 9 10 . It is apparent that, because loss of vision is the first presenting symptom of Batten disease, the eye is an ideal system for the study of the primary molecular events associated with the CLN3 defect. 
Cln3-knockout mice homozygous for a targeted deletion of exon 1 to 6 in the Cln3 gene have been reported to show characteristic accumulation of autofluorescent lipopigments containing mitochondrial ATP synthase subunit c in neural tissue and selective loss of γ-aminobutyric acid (GABA)ergic neurons. 11 We have previously reported gene expression changes in the cerebellum of 10-week-old Cln3-knockout mice. 12 13 To gain insight into gene expression changes that associate with the CLN3 defect, we repeated our gene expression study in the whole eye of the Cln3-knockout mouse. We classified genes displaying an altered expression pattern into 13 functional categories based on functional information associated with the gene product. The altered gene expression pattern in Cln3-knockout eye shows that there are 285 genes that are either up- or downregulated. By comparing these gene expression data with those previously reported in the cerebellum we were are able to identify 18 genes with a change in expression that is specific to the eye. This data set provides an important comparative analysis of the CLN3 defect. 
Materials and Methods
Animals
Ten-week-old wild-type control 129S6/SvEv and homozygous Cln3-knockout mice on a 129S6/SvEv background 11 were used in the study. All procedures were performed in accordance with NIH guidelines and University of Rochester Animal Care and Use Committee Guidelines. Furthermore, all research conformed to ARVO Standards for the Use of Animals in Ophthalmic and Vision Research. 
Gene Expression Studies and Data Analysis
For comparative gene expression studies whole eyes from three each of the 10-week-old wild-type control and Cln3-knockout mice were pooled and homogenized by standard procedures (TRIzol; Invitrogen-Gibco, Grand Island, NY) for mRNA extraction. Total RNA (10 μg) from each sample was used to generate a high-fidelity cDNA, which is modified at the 3′ end to contain an initiation site for T7 RNA polymerase, as per the manufacturer’s protocol (SuperChoice; Invitrogen-Gibco). On completion of cDNA synthesis, 1 μg of product was used in an in vitro transcription (IVT) reaction that contained biotinylated UTP and CTP, which will be used for detection after hybridization to the microarray as per the manufacturer’s protocol (Enzo Biochemicals, Farmingdale, NY). Full-length IVT product (20 μg) was subsequently fragmented in 200 mM Tris-acetate (pH 8.1), 500 mM KOAc, and 150 mM MgOAc at 94°C for 35 minutes. After fragmentation, all components generated throughout the processing procedure (cDNA, full-length cRNA, and fragmented cRNA) were analyzed by gel electrophoresis to assess the appropriate size distribution before microarray analysis. 
All samples represented were subjected to gene expression analysis using the a high-density oligonucleotide array set (Mu19K; Affymetrix, Santa Clara, CA), at the University of Rochester Microarray Core Facility, as previously described. 12 The mathematical definitions for the algorithms can be found in the Microarray Suite Analysis manual in the algorithm tutorial. The change ratio of expression of any transcript between baseline and experimental is calculated after global scaling. All data represented from this first approach are from pair-wise comparison analyses. 
Reverse Transcription–Polymerase Chain Reaction
Validation of gene expression changes was performed for GAPDH, glutaminase C, lipidosin, protein synthesis initiation factor 4A (ELF41A), neuroendocrine differentiation factor (NEDF), ATP-synthase subunit B, and the unknown transcript identified as TC36735 by probe set numbering (Affymetrix). RNA extracts prepared for the gene chip studies (GeneChip; Affymetrix) were used. Amplification of a portion of each gene was performed with 1 μg total RNA (SuperScript Two-Step RT-PCR system with SYBR green; Invitrogen-Life Technologies, Gaithersburg, MD, on a Prism system; Applied Biosystems [ABI], Foster City CA), according to the manufacturers’ guidelines. Primers used for amplification are described in Table 1
Histology
Eyes were removed from the mice and fixed in 4% paraformaldehyde for 3 hours, to harden the tissue and prepare it to be sectioned. The eyes were then dehydrated 100% in an ethanol gradient and placed in xylenes. They were put into a 1:1 mixture of melted paraffin and xylenes at 60°C and were then moved to pure paraffin, where it permeated the tissue. The cassette containing the embedded eye was placed on a paraffin microtome (Leica Microsystems, Bannockburn, IL) and cut into 6-μm sections. Sections were deparaffinized and allowed to dry overnight, hydrated to 70% ethanol, and stained with hematoxylin I and eosin Y (H&E). For autofluorescence imaging, sections were cleared with xylenes and mounted (Permount; Fisher Scientific, Pittsburgh, PA). Digital images were taken with a camera (Spot camera; Diagnostic Instruments, Sterling Heights, MI) mounted on a microscope (Olympus Corp. of America, Lake Success, NY). A 4× objective captured the whole eye, and the 40× objective was used to obtain detailed images of the peripheral retina. Fluorescence images were taken through a 488-nm filter. Images were cropped and background removed (Photoshop; Adobe Systems, Mountain View, CA). 
Results
Batten disease is a lysosomal storage disease with accumulation of autofluorescent lipopigment in the lysosomes of individuals with the disorder. Homozygous Cln3-knockout mice have been confirmed to have similar accumulation within the brain and eye. 11 14 15 As the eye is one of the first regions of the central nervous system (CNS) to deteriorate in Batten disease, we compared gene expression in the eye of 10-week-old normal and Cln3-knockout mice. In this initial study we took the whole eye from Cln3-knockout and wild-type control mice and examined gene expression changes associated with the CLN3 defect. To maximize interpretation of data obtained on changes in gene expression that are associated with the CLN3 defect, we compared the data obtained from this study to those in a previous experiment, in which we compared gene expression changes in cerebellum of 10-week-old normal and Cln3-knockout mice. 
Characteristics of 10-Week-Old Cln3-Knockout Eyes
It has been shown that cln3-knockout mice demonstrate the characteristic presence of autofluorescent storage material in the retina at 12 months of age. 15 Although wild-type control animals also demonstrate the presence of storage material, there is a clear elevation in the cln3-knockout retina. We considered that an ideal time to perform gene expression studies in the eye of cln3-knockout mice would be at a point when this pathologically characteristic storage material first appeared in cln3-knockout, but not in wild-type, animals. Figure 1a shows that the retina of 10-week-old cln3-knockout mice seemed to be normal and resembled that of an age-matched wild-type control. The thickness of the each cell layer appeared to be the same, with no obvious cell loss. In Figure 1b , autofluorescent storage material was beginning to appear or accumulate in the retina, particularly in the inner nuclear layer and ganglion cell layer, at 10 weeks of age in cln3-knockout, but not in the wild-type control. 
Altered Gene Expression in Cln3-Knockout Eye
Gene expression was assessed in the eye of 10-week-old mice to explore changes in transcription that may precede degenerative changes. To minimize variation, eyes were collected from three 10-week-old male Cln3-knockout and three age-matched male wild-type control mice, and the material from each genotype was pooled for extraction of mRNA. Duplicate independent samples for both control and Cln3-knockout mice were also prepared from another six animals. This essentially provided two sets of mRNA from both wild-type control and Cln3-knockout eyes, to allow a four-way comparison of gene expression between control and the Cln3-knockout. The resultant probes derived from these mRNA sets were hybridized to high-density Mu19 subarrays A, B, and C (Affymetrix). 
Comparison of two Cln3-knockout samples to both wild-type samples allows for a four-way comparison for statistical evaluation. Previous studies have validated changes in gene expression in this system obtained using gene chips (Affymetrix) by semiquantitative RT-PCR. 13 We therefore focused our analysis on comparing the molecular profiles of the CLN3 defect between eye and cerebellum. 
Functional Classification of Genes with Altered Expression
We assigned a functional class to all 285 genes that had a reproducible change in expression of twofold or more (Table 2) . We chose a twofold change in expression as our cutoff, because we considered at least a doubling or halving of the level of a transcript to be an arbitrary way of determining significance. 1 In characterizing the genes with altered expression, many could clearly be assigned to more than one functional class, due to having either more than one function, or because there is overlap between the functional classes themselves. For the sake of clarity, we assigned each gene to only one functional class based on information in the literature on the function of each gene product. These functional classes are based on the protein having a function in (1) signaling or cell growth; (2) cell structure, cell adhesion, or at the cell surface; (3) proteolysis or inhibition of proteolysis; (4) neuronal cell development and function; (5) lipid metabolism; (6) immune or inflammatory response; (7) energy metabolism; (8) detoxification or stress; (9) cytoskeleton; (10) cell death; (11) vascular and blood; (12) amino acid metabolism; (13) unknown, based on there being no known function of the protein, or in a small number of cases, our inability to fit the protein into any of the 12 classes. The classification of gene products and data on their altered expression is presented in Table 2 . This table presents the mean change ratio, and does not include the data on the change ratio for each comparison. The entire data set can be viewed on the Internet at http://dbb.urmc.rochester.edu/laboratories/pearce/microarray.html. 
Genes with Altered Expression Specific to the Eye
To aid our understanding of the expression changes we see in the eye of the Cln3-knockout mice we compared the data to that obtained for expression changes in the cerebellum. We previously reported gene expression changes of twofold or more in cerebellum of 10-week-old Cln3-knockout mice. 1 In Table 3 , we list the 18 genes that are unique to the expression data obtained from the eye only. In other words, genes that had altered expression in the cerebellum as well as the eye have been excluded from this list. We selected six of these genes for validation by RT-PCR compared with control GAPDH expression, which is unchanged in cln3-knockout compared with normal (Fig. 2) . We demonstrated that transcripts for glutaminase C and an unknown transcript designated TC36735, which had had a 6.2- and 14.0-fold increase in expression by microarray analysis, respectively, had a 3.6- and 7.3-fold increase in expression by RT-PCR, respectively. Similarly, NEDF, lipidosin, ELF4A, and ATP-synthase subunit B which had respective decreases in expression of −4.0, −15.5, −38.7, and −4.9 by microarray analysis had decreased expression of −1.9, −8.0, −8.3, and −3.5 by RT-PCR, respectively. Collectively, each validation confirms a significant change in expression of these transcripts in the same direction as predicted by the microarray. We tested expression of each of these transcripts in cerebellum and whole brain of 10-week-old cln3-knockout and wild-type control mice and saw no difference in expression. 
Discussion
Batten disease is a devastating neurologic disorder, and, as with many disorders, the mechanism that results in vision loss and the neurodegenerative course is poorly understood. Although the Cln3-knockout mouse has many of the pathologic characteristics of Batten disease, and we show in this report the appearance of the characteristic storage material at 10-weeks of age, it does not have an apparent loss of vision. 15 The gene expression data we report will prove valuable as we gain further insight into the mechanisms that may predicate the appearance of autofluorescent storage material and perhaps vision loss in this and other diseases. The functional classes of genes that have altered expression in Cln3-knockout eyes compared with wild-type control eyes can be used to hypothesize about the biological differences that may be present. With 285 reproducible changes in expression reported, many biological processes are disturbed in the eyes of 10-week-old Cln3-knockout mice. Moreover, it is very interesting that their eyes have such a shift in gene expression compared with wild-type control mice. If we look at each functional group, most categories have more transcripts upregulated than downregulated. For example, genes involved in proteolysis, both for degradation (for example, cathepsin L) and inhibition of degradation (for example, stefin 3) are predominantly upregulated. Similarly, 14 (74%) of 19 of transcripts associated with the cytoskeleton (for example, β-tropomyosin and troponin) are upregulated. All transcripts associated with cell structure, cell adhesion, and the cell surface are also up regulated, and along with the changes observed in proteolysis and the cytoskeleton, may predict that intracellular and extracellular integrity of the cells is somewhat compromised. The neuronal cell development and function class reveals that many genes are up- and downregulated. It is of interest that a number of genes associated with cell death (for example, p53 and DAP1) are also upregulated, suggesting that a certain number of cells may have been programmed to die. 
All but one gene in the detoxification and stress functional class are upregulated, which is consistent with what may be predicted about the diseased state resulting in cellular damage. Up- and downregulation of several genes associated with energy metabolism is also apparent, some of which are associated with mitochondrial function (for example, cytochrome oxidase and subunit B of ATP-synthase). The role of mitochondria and energy metabolism in Batten disease is particularly interesting in view of the emphasis placed on the role of mitochondrial dysfunction in this disease in many other studies (for review, see Ref. 16 ). A hallmark of Batten disease is accumulation of ATP synthase subunit C in the lysosome; thus, it is interesting that there is an apparent downregulation of a different subunit of this complex and ATP synthase B-subunit. Many genes associated with lipid metabolism are up- and downregulated, and detailed analysis of these events may contribute to our understanding the composition of accumulating lipopigments in the Batten disease and the molecular mechanisms underlying their deposition. Overall, these findings suggest that Cln3-knockout mice have a major change in the biology of the cells within the eye. The fact that there is such a large number of changes in gene expression compared with wild-type control animals suggests that molecular events associated with the CLN3 defect occur before the appearance of autofluorescent storage material in 10-week-old Cln3-knockout mice. 
Because there are several cell types in the eye, it is not possible to identify whether subsets of cells or all cell types experience the gene expression changes we report. These gene expression data present an overall picture of a vast set of molecular changes that result from a lack of the CLN3 protein and provide a valuable data set for researchers for further exploration of the pathogenesis of the disease and for cell-type–specific changes in gene expression. There are 18 genes with altered gene expression in the eye that are not evident in the previously reported data set on altered expression in the cerebellum. 12  
It is apparent that 13 (72%) of 18 of the genes with an altered expression pattern in the eye only are downregulated. However, it is important to note that this is based on those transcripts that were detectable in the samples and present on the microarrays used. Nevertheless, three of these are a part of complexes in the mitochondria that contribute to energy production: cytochrome oxidase, cytochrome B, and ATP synthase. It has been suggested that mitochondrial dysfunction could precipitate cell death in NCL. 17 If cell types in the eye are more susceptible to the CLN3 defect, the changes we report in expression of mitochondrial proteins involved in energy production is also suggestive that mitochondrial dysfunction is a part of the degenerative process. It is also fascinating that ATP synthase subunit B is downregulated, when another component of this complex, subunit C, is a major component of the storage material that accumulates in the lysosome. This observation fits with previous reports of decreased activity of ATP synthase and decreased mitochondrial function in NCL and that perhaps there is coordinate regulation in the expression of ATP-synthase subunits. 18 19 20 21 As more microarray data sets on the expression of genes in the eye and certain cell types within the eye become available, a more detailed interpretation of the CLN3 defect on different cell types will be possible. 
 
Table 1.
 
Primers Used for RT-PCR Validation of Expression Levels
Table 1.
 
Primers Used for RT-PCR Validation of Expression Levels
Transcript Primers
GAPDH 5′-GCTCCCTAGGCCCCTCCTG-3′
5′-CAAGAAGGTGGTGAAGCAGGCCAC-3′
Glutaminase C 5′-TAACTGCTAGTATCTGTGCA-3′
5′-AAGAGATAAAGGGTATGTT-3′
Lipidosin 5′-GAAGCTCGGCCTAGAGCGTG-3′
5′-TATGAGCTCCTCCATCGTGT-3′
ELF41A 5′-TTATATGGGAGCAACTTGTC-3′
5′-TTGGTCACTTCTAGCACATC-3′
NEDF 5′-AGTGAAAGATGCAGCCAAGA-3′
5′-ATCGCTCCTGCGGGTTCA-3′
TC36735 5′-GAAACTTGTCTAATACCAG-3′
5′-GACAGTTGTCACCATGAGA-3′
ATP-synthase subunit B 5′-TATGTGCTTGGAACTGGACT-3′
5′-CACTAAGTGGACCTTGATCT-3′
Figure 1.
 
(a) Comparison of gross morphologic changes in 10-week-old cln3-knockout and wild-type control mice. Micrographs were taken with a 40× objective and show a representative subsection of the retina with the ganglion cell layer (GCL) on the bottom of the image. (b) Comparison of autofluorescence in 10-week-old cln3-knockout and wild-type control. Photographs were taken with a 40× objective in representative subsection of the retina with the GCL at the bottom of the image. The inner and outer segments of the photoreceptors, which autofluoresce naturally, have been cropped from these images. ONL, outer nuclear layer; OPL, outer plexiform layer; INL, inner nuclear layer; IPL, inner plexiform layer.
Figure 1.
 
(a) Comparison of gross morphologic changes in 10-week-old cln3-knockout and wild-type control mice. Micrographs were taken with a 40× objective and show a representative subsection of the retina with the ganglion cell layer (GCL) on the bottom of the image. (b) Comparison of autofluorescence in 10-week-old cln3-knockout and wild-type control. Photographs were taken with a 40× objective in representative subsection of the retina with the GCL at the bottom of the image. The inner and outer segments of the photoreceptors, which autofluoresce naturally, have been cropped from these images. ONL, outer nuclear layer; OPL, outer plexiform layer; INL, inner nuclear layer; IPL, inner plexiform layer.
Table 2.
 
Expression Changes Greater Than 2 in Cln3-Knockout Eye, Compared with Wild-Type Control
Table 2.
 
Expression Changes Greater Than 2 in Cln3-Knockout Eye, Compared with Wild-Type Control
Average Change TIGR/Affymetrix No. Annotation
Amino acid metabolism
 22.475 TC39031_at Arginase
 16.925 TC29651_at Possible deaminase
 4.125 TC19442_at Cysteine dioxygenase
 −3.05 TC37346_g_at L-asparaginase
 −4.925 TC28329_g_at NBAT
 −5.325 TC30372_f_at Glutamate dehydrogenase
 −6.15 TC40291_at Tryptophan dioxygenase
 −7.1 TC33164_at Glycine amidotransferase
 −8.375 TC31560_s_at D-aminoacid oxidase
 −20.175 TC24073_at Possible arginine decarboxylase
Blood/vascular
 129.45 TC27670_g_at Myoglobin
 37.075 TC40225_s_at Transthyretin like protein
 23.25 TC32287_at hbr3 brain carboxyesterase
 13.075 TC34069_at Carbonic anhydrase III
 3.425 TC35644_s_at FCK1, VEGF binding, vasculogenisis
 −19.725 TC24493_at Electrogenic Na bicarbonate cotransporter (NBC)
Cell death
 322.8 TC17513_at Death asociated protein DAP1
 158.25 TC37556_at p53 protein
 122.3 TC19787_at p53 apoptosis-associated target
 88.625 TC24816_s_at DAP1 death associated protein
 24.45 TC16227_at Similar to death receptor 6
 20.275 TC15396_at Early quiescence protein-1
 15.825 TC19399_at Apoptosis associated speck protein P(YCARD)
Detox/stress
 32.55 TC40306_f_at Glutathione transferase
 22.85 TC41370_s_at HSP70
 12.2 TC29966_g_at Ceruloplasmin
 4.825 TC35139_at HSBX, heat shock protein, like HSP20
 4.6 TC31120_f_at Plasma glutathione peroxidase
 4.475 TC21222_at Unknown
 −31.325 TC29829_at HSC73
Energy metabolism
 122.7 TC18565_i_at Cytosolic malate dehydrogenase
 48.375 TC15436_s_at Cytochrome c oxidase subunit VIIa-H precursor
 34.575 TC20349_at Creatine kinase
 11.3 TC32389_at PHS1. glycogen phosphorylase
 10.875 TC32884_f_at Lactate dehydrogenase
 7.475 TC23942_i_at Creatine kinase
 6.95 TC19057_g_at Phosphoglycerate mutase muscle-specific subunit
 6.85 TC37832_at Glycogenin-1
 2.825 TC28383_s_at Glucose-6-phosphate dehydrogenase
 −3.425 TC40415_at Cox1, cytochrome oxidase I
 −3.475 TC30467_at NADH dehydrogenase subunit 5
 −4.35 TC38446_g_at Cytochrome oxidase subunit 1
 −4.85 TC19304_at ATP synthase B-subunit
Signaling/Cell Growth
 63.2 TC36530_g_at Mnk2, map kinase interacting kinase
 27.6 TC18256_at Protein kinase Dyrk2
 17.5 TC29599_at TC21 protein
 5.225 TC36530_at Mnk2
 3.825 TC26799_i_at mPRL-3 tyrosine kinase
 3.525 TC34509_g_at MEKK 1, map kinase
 3.275 TC35395_at Caveolin-2
 2.65 TC21379_at RhoGAP, GTPase activating protein
 −2.9 TC21250_g_at Serine/threonine phosphatase 2B
 −2.95 TC25040_at p54, JNK-2, stress activated kinase
 −3.05 TC15005_s_at SHIP2, inositol polyphosphate phosphatase
 −8.1 TC38592_g_at cGMP phosphodiesterase type A9
 −8.5 TC16846_s_at bfgf-r, basic fibroblast growth factor receptor-1
 −9.3 TC15262_at Phosphodiesterase I
 −10 TC34425_g_at fyn(T), tyrosine kinase
 −11.725 TC25522_s_at PCTAIRE-I serine/threonine kinase
 −12.1 TC15645_s_at Inositol 5-phosphatase
 −12.425 TC18155_s_at fyn(T), tyrosine kinase
 −24.65 TC33667_at SPOT14, thyroid hormone inducible protein
 −54.25 TC36931_at Phosphatallic acid phosphotase 2c
Lipid metabolism
 382 TC27653_at 3-ketoacyl-CoA thiolase B
 33.75 TC19057_at Phosphoglycerate mutase muscle-specific subunit
 20.175 TC15810_s_at 3-oxoacyl-CoenzymeA thiolase, mitochondrial
 15.15 TC37551_at Paraoxonase 2 (PON2)
 6.35 TC14864_f_at Keratinocyate lipid-binding protein
 4.85 TC16399_f_at Acyl-CoA dehydrogenase
 4.35 TC33350_at Putative C-8,7 Isomerase
 3.725 TC35242_s_at Heme oxygenase
 −4.875 TC38739_at Diacylglycerol kinase
 −5.05 TC15835_at Oxysterol binding protein
 −5.85 TC37906_s_at Delta-G fatty acid desaturase
 −5.875 TC22730_s_at b-fabp, brain fatty acid binding protein
 −58.775 TC33071_s_at AcylcoA desaturase 2
Protease
 93.35 TC26009_at Stefin 3
 91.05 TC39719_f_at Mac-2, lactose binding lechin
 39.9 TC22206_at CYT4, stefin homolog
 16.8 TC31277_at Serine protease
 14.675 TC35575_at Epithln serine protease
 12.85 TC21695_at Similar to serine proteases
 12.8 TC33498_at Nephrilysin like peptidase
 12.7 TC17364_at Prostasin
 8.275 TC34450_at Aminopeptidase
 7.95 TC34175_at Like aminopeptidase
 6.925 TC16079_at Similar to neurotrypsin
 2.975 TC32493_f_at Cathepsin L
Structural/adhesion/cell surface
 50.9 TC25512_s_at F1SP12 protein, tissue growth factor
 47 TC22866_f_at Collagen alpha-1
 37.85 TC19711_s_at 57 kd keratin
 30.375 TC26960_at Keratin 6 alpha
 28.475 TC30949_at Claudin 7
 26.4 TC24005_s_at Cytokeratin 4
 21.05 TC40219_at VLA-6
 16.75 TC18507_f_at Decorin
 8.825 TC24347_s_at Cytokeratin 13
 8.3 TC33778_i_at Collagen alpha 1
 7.05 TC16852_at Periplakin
 6.825 TC41987_at Desmocollin type 2
 4.9 TC14593_s_at Collagen alpha -2
 4.75 TC40853_f_at Collegan alpha 1
 3.775 TC37852_at Junction adhesion protein
Immune
 137.775 TC23274_at 14-3-3 protein sigma
 132.1 TC20347_at Prostate stem cell antigen
 92.175 TC36394_f_at Galectin-1
 80.725 TC26633_g_at UCP2
 63.725 TC15466_f_at Lipocortin I
 43 TC34607_s_at DBPA homolog
 40.8 TC39759_at TB2 like
 36.2 TC37183_s_at TRP2, dopachrome taulomerase
 33.325 TC40399_s_at Hepatitus virus receptor
 17.8 TC40929_s_at Beta interferon induced protein
 16.575 TC34649_at Similar to IC2
 10.75 TC24304_g_at Linear IgA disease antigen homolog
 8.85 TC25579_at Oncostatin M receptor beta
 7.05 TC14570_f_at C1 inhibitor
 6.425 TC41813_f_at STAT6
 6.275 TC18855_f_at Catpactin 1 light chain
 6.225 TC35184_f_at Macrophage capping protein
 6.2 TC24577_at XLR 4 lymphocyte regulatory protein
 5.925 TC19499_s_at Myc basic motif homologue-1
 5.7 TC24581_at Interferon activatable protein
 4.9 TC28116_g_at DOPAchrome tautomerase
 4.825 TC34110_at LYVE-1, tymphatic endolithium specific receptor
 4 TC15924_at LAR, lenkocyte common anitgen protein
 3.7 TC14368_f_at Lipocortin II / Annexin II (anxII)
 −3.125 TC23291_s_at HUD paraneoplastic antigen
 −3.35 TC36543_at Similar to paraneoplastic antigen, KIAA0883
 −3.7 TC33860_at Neuronal IL-16
 −3.875 TC37323_at Similar to Iga regulatory protein
 −4.1 TC32923_s_at Corticosteroid II-beta dehydrogenase
 −5.15 TC17814_at Corticotropin releasing hormone receptor 2
 −49.575 TC26088_at BM88 antigen
Neuronal cell develepment and function
 294.375 TC32454_at Similar to maxi-K channel
 286.325 TC20337_at Similar to synapsin 1
 75.925 TC16591_at Proleo lipid protein 2
 66.05 TC33406_s_at Peripheral benzodinzepine receptor (ptr)
 64.625 TC30567_s_at Syndecan-1
 60.75 TC36687_at Protein 4.1G
 48 TC19521_g_at Nuclear pore-targeting complex component of 58 kDa
 31.85 TC37537_at Protein 4.1G
 30.1 TC36143_g_at Ezrin
 26.1 TC32955_s_at Els transcription factor
 20.025 TC31586_at Syntaxin 3
 14.575 TC25273_at Dystonin; BPAG-1
 13.225 TC24557_at Dkk-3, dickkopf-3
 12.375 TC30575_at SIX3 protein
 11.1 TC22048_at Semaphorin IV isoform a
 10.45 TC40712_at Connexin 46
 6.625 TC40937_s_at UNC119/ HRG4
 4.125 TC41353_at Glypican 3
 3.725 TC36142_at Ezrin
 3.225 TC41791_at PACSIN2 (syndapin IIaa)
 3.075 TC36827_at Cerebellum postnatal protein-1
 −2.925 TC38522_at KIAA0916 human protein, highwine in drosophila
 −3.05 TC14267_i_at RKIP, phosphoatidylethandlumne binding protein
 −3.175 TC17976_at rsk2, calcium activated K-channel
 −3.2 TC32675_s_at Myelin gene expression factor, myef-2
 −3.225 TC37684_at Kinesin light subunit B, (KLC)
 −3.5 TC26270_s_at KIFI, kinesin like
 −3.525 TC39656_f_at Neuritin
 −3.55 TC41874_at ndr2
 −3.725 TC22759_at Calcineurin b.
 −3.975 TC38290_at Neuroendocrine differentiation factor
 −4.05 TC16990_s_at Neural vision like protein
 −4.275 TC34140_s_at Alpha-catenin (alpha -e)
 −4.3 TC26822_at Acrogranin
 −4.675 TC24292_at ATN2, Na/K transporter subunit 2
 −4.8 TC30767_at SCHIP-1
 −6.325 TC37996_at DARPP-32
 −6.45 TC31890_g_at Secretogranin III
 −7.275 TC39376_at Pro SSAS
 −7.4 TC18154_at Brain development protein BDM1
 −7.8 TC39160_g_at SCG10
 −8.475 TC22283_s_at PLP, myelin proteilipid
 −9.85 TC36359_at TREK-1 K+ channel subunit
 −9.95 TC29998_at Myelin basic protein
 −10.025 TC39061_at Hippocampal amyloid precursor protein (beta)
 −11.65 TC14881_at SCG10
 −13.825 TC24570_at Na/K transporting ATPase, alpha 2 subunit
 −15 TC30390_s_at p21, neuron specific protein
 −16.925 TC18867_at Alpha synuclein
 −18.1 TC39041_at Nel proptein
 −18.9 TC26003_at Synaplogamin XI
 −19.175 TC37308_at Double cortin like protein
 −19.625 TC22741_g_at Neuronal specific septin-3
 −20.625 TC30389_f_at p21, neuron specific protein
 −20.925 TC35356_at Neurilin
 −21.25 TC18648_at NFI-x nucleus factor
 −22.35 TC36040_at Like GCAP1, granule cell marker protein
 −29.375 TC15940_g_at Coat protein gamma cap.
 −48.05 TC22429_s_at Myelin proteolipid protein (PLP)
 −74.375 TC17234_s_at Calbindin
Cytoskeleton factors
 158.975 TC15490_s_at Troponin T fast skeletal muscle isoform
 109.95 TC18963_g_at Beta-tropomyosin
 66.975 TC40898_f_at Troponin 1
 29.275 TC28732_s_at Myosin heavy chain 2a
 19.65 TC19756_at Actin-related protein complex 1b
 15.95 TC22827_at Tropomyosin alpha
 14.325 TC33465_g_at Myosin light chain 1
 13.85 TC15815_at Alpha-actin
 13.725 TC22502_f_at Myosin light chain 2
 12.925 TC28358_f_at Myosin regulatory light chain
 12.5 TC40908_at Tubulin beta 5 subunit
 7.825 TC32100_s_at Alpha actinin -4
 4.025 TC29413_f_at Myosin heavy chain 2B
 3.85 TC39600_f_at Getsolin
 −3.225 TC18165_g_at Prefoldin subunit
 −3.575 TC21995_g_at Microtubule associated protein, tan
 −4.15 TC18613_at Like novel protein c380A1,2.2.
 −4.775 TC20757_s_at ANK-3
 −28.625 TC38163_f_at Tubulin beta-3
unknown
 224.275 TC27018_f_at Gamma 4-crystallin (aa 85-174): gamma-A-crystallin
 121.075 TC27118_at Beta-A4-crystallin
 116.9 TC23815_s_at Mouse fast skeletal muscle SR calcium ATPase
 94.75 TC29087_s_at Unknown
 90.65 TC16275_at Ataxia-telangieclasia group D-associated protein
 86.475 TC15537_f_at Folate-binding protein 1
 79.925 TC23172_at Unknown
 67.825 TC20950_at mCBP
 62.075 TC34763_at Unknown
 57.15 TC16425_s_at Unknown
 52.55 TC18741_f_at Unknown
 44.025 TC37929_at Unknown
 42.8 TC14369_f_at Protein-tyrosine kinase substrate
 39.4 TC16278_at Gamma-C-crystallin
 37.725 TC15584_at Unknown
 36.725 TC32177_at Unknown
 36.725 TC23979_g_at Unknown
 33.5 TC34356_at Unknown
 33.275 TC31887_at Possible glycoprotein
 33.075 TC22352_s_at s100-type calcium binding protein
 32.475 TC26873_at Beta-A3/A1 crystallin
 32 TC30868_f_at PABP polyA binding protein
 31.3 TC31507_at 5100-type calcium binding protein
 29.8 TC36511_at Unknown
 28.275 TC17811_at Unknown
 28.2 TC40393_s_at Calcium binding protein
 27.525 TC41119_at Unknown
 26.875 TC23617_f_at Histone H1
 26.825 TC24011_at Unknown
 26.225 TC27544_at Possible kinase
 25.675 TC20429_at GSG1
 25 TC42144_at Dithiolethiume induced gene
 24.75 TC16184_g_at Unknown
 23.7 TC33945_at Unknown
 23.45 TC30861_at Hepatocellular carcinoma-associated antigen 112
 23 TC37660_s_at Like undine kinase
 21.875 TC37456_at Unknown
 21.8 TC16584_g_at Unknown
 21.3 TC20216_at Unknown
 20.7 TC38463_g_at Onzin
 20.525 TC37769_g_at Unknown
 20 TC38105_at A mannosylglycoprotein b 1–6 acetyl glucosaminyl transferase
 18.2 TC40398_g_at BGP-1 glycoprotein
 17.8 TC39732_at Unknown
 17.65 TC40856_at P8 protein
 16.95 TC22847_s_at Aldose reductase-related protein 1
 16.55 TC22660_at Unknown
 15.825 TC21363_at Unknown
 15.075 TC40330_at Unknown
 14.85 TC37670_g_at Unknown
 14.275 TC21338_at Unknown
 14.075 TC33781_at Unknown
 13.975 TC36735_g_at Unknown
 13.475 TC35151_at Unknown
 13.4 TC37498_g_at Similar to TITIN
 13.35 TC35267_at Unknown
 12.525 TC32779_at Unknown
 12.275 TC22217_g_at Gamma-sarcoglycan
 12.05 TC21382_at Unknown
 11.75 TC38572_at Like KIA0009
 11.225 TC28227_at BM-003
 11.2 TC15010_at Ataxia-telangieclasia group D-associated protein
 10.95 TC40893_f_at Alpha crystallin B-chain
 10.8 TC35947_at Secreted modular calcium binding protein
 10.7 TC42043_s_at Unknown
 10.525 TC35166_at Unknown
 10.35 TC31979_at Unknown
 10.325 TC40743_s_at Transketolase
 10.025 TC24736_at Unknown
 9.8 TC32729_at Unknown
 9.1 TC14992_i_at Double LIM protein-1
 9.05 TC34343_at Unknown
Eye unknown
 8.95 TC31534_g_at RNA binding protein RBP, MS
 8.7 TC37405_at Possible glycoprotein
 8.575 TC34789_at Like echinoderm microtubule associated protein
 8.45 TC41574_g_at Unknown
 8.25 TC40445_at Unknown
 8.1 TC31394_g_at Unknown
 7.425 TC16738_at Cell growth regulating nuclear protein
 7.175 TC35223_g_at Hopotocyte growth factor activator
 6.975 TC19085_f_at Histone H2a 1-F
 6.975 TC19105_g_at Unknown
 6.7 TC16842_at Unknown
 6.675 TC30935_at Unknown
 6.65 TC15420_g_at TGF-beta-inducible protein
 6.625 TC41695_at Unknown
 6.6 TC41312_at Unknown
 6.425 TC36884_at Signal transducer of transcription activator 6
 6.375 TC33908_at Unknown
 6.2 TC28305_at Unknown
 6.175 TC40703_at Unknown
 6.075 TC21210_at Like SIAP-2 sarolemmal associated protein
 6.05 TC22993_s_at Like BM-019
 6.025 TC30968_at Unknown
 5.925 TC38179_at NX-17
 5.75 TC16584_at Unknown
 5.725 TC39835_at Unknown
 5.575 TC31268_at Unknown
 5.575 TC31974_s_at Hapatocyte growth factor activator inhibitor
 5.525 TC35180_at UROPLAKIN IB (UP18)
 5.45 TC34662_g_at FGF binding protein 1
 5.45 TC39762_at Unknown
 5.25 TC22472_g_at Insulin-like growth factor binding protein-4, IGFBP-4
 5.1 TC32825_at Unknown
 5.1 TC15512_at Unknown
 5.05 TC16200_at Unknown
 5.025 TC26659_f_at Gamma E crystallin
 5.025 TC33445_at SM-20, growth factor responsive protein
 5 TC31101_g_at NX-17
 4.95 TC32986_g_at SGLT1 sodium glucose transporter-1
 4.925 TC28395_at Unknown
 4.75 TC39257_g_at Unknown
 4.75 TC41820_f_at pnbp1, poly a binding protein
 4.725 TC33957_f_at Unknown
 4.7 TC16337 s at Aldose reductase-related protein 1 reductase
 4.7 TC38699_at Unknown
 4.55 TC39978_at Unknown
 4.475 TC23656_g_at HSP 70
 4.45 TC16809_at Sialomucin MGC-24
 4.425 TC34081_at Unknown
 4.275 TC32695_a_at TtSII B
 4.15 TC25859_at Unknown
 4.025 TC34228_g_at Unknown
 4 TC40849_at KIAA 1561 like
 3.775 TC36904_g_at Unknown
 3.775 TC41912_at Unknown
 3.725 TC41574_at Unknown
 3.7 TC33236_f_at Collagen alpha-2
 3.675 TC38758_at Similar to ribonuclease
 3.65 TC40553_at Predicted osteoblast protein G53786
 3.525 TC16880_at Unknown
 3.5 TC41930_at ZNT4 zinc transporter 4
 3.425 TC18373_at Unknown
 3.425 TC36701_at MEA1 antigen
 3.425 TC37498_at Like title
 3.4 TC33329_at Cavaolio-1
 3.35 TC28712_at Unknown
 3.325 TC26918_i_at Ocant-binding transcription factor I (cbta)
 3.275 TC35003_s_at Initiation factor
 3.25 TC17314_at Unknown
 3.175 TC28860_at Unknown
 3.175 TC28860_at Unknown
 3.15 TC30867_at PAB1, polyadcnytate binding protein
 3.125 TC34228_at Unknown
 3.1 TC33264_at Guanine nucleotide binding protein
 2.925 TC22848_s_at UBC3
 2.9 TC28660_g_at Unknown
 2.7 TC34620_f_at Ribosomal protein 520
 −2.8 TC14392_f_at Stathmin
 −2.85 TC18861_at Unknown
 −2.85 TC24550_at Unknown
 −2.925 TC39474_f_at Lactate dehydrogynase
 −2.975 TC33078_at Unknown
 −3 TC41056_at Unknown
 −3.125 TC32289_a_at ABC2
 −3.175 TC18736_g_at Protein synthesis initiation factor 4A, ELF41A
 −3.175 TC29636_at Unknown
 −3.175 TC41293_at Unknown
 −3.2 TC41345_at Unknown
 −3.225 TC17259_g_at Unknown
 −3.225 TC20592_at Small nuclear ribonucleo protein, SmO
 −3.25 TC34446_at Unknown
 −3.275 TC16825_at Unknown
 −3.275 TC24812_at Unknown
 −3.3 TC39752_at Unknown
 −3.3 TC40014_at Unknown
 −3.35 TC25091_at Transcription repressor RPS8
 −3.35 TC38493_at Unknown
 −3.35 TC22066_at Unknown
 −3.4 TC33205_at SERCA 2n
 −3.425 TC28327_at Similar to EXTL2 human
 −3.5 TC15898_f_at Similar to LDOC1 human
 −3.5 TC22782_g_at Similar to cadherin 22
 −3.525 TC22801_at PAK-1 threoniae/serine kinase p21 activated
 −3.575 TC35044_at Unknown
 −3.65 TC25610_s_at Neodin
 −3.7 TC37065_at Same as FCJ10856 human protein
 −3.875 TC27925_i_at Plallet activating factor PAF acatythydroinse
 −3.95 TC29662_at Unknown
 −3.975 TC22817_at Brain protein 154
 −4.05 TC38604_at Unknown
 −4.075 TC18152_at Unknown
 −4.075 TC38584_at KIA1583 human protein
 −4.125 TC34542_at Ribonucleoprotein A2/B1
 −4.15 TC19732_at Unknown
 −4.3 TC33029_g_at Unknown
 −4.3 TC37489_a_at Mouse brain protein, BH5, peanut-like
 −4.475 TC39750_at Unknown
 −4.525 TC39858_at Unknown
 −4.55 TC34778_at Unknown
 −4.575 TC38646_at KIA0436, human, like oligopeptidase
 −4.6 TC26109_at Unknown
 −4.6 TC36755_at Neural membrane glyco protein, M6–8
 −4.7 TC39581_at Unknown
 −4.725 TC22193_at Transcriptional repressor RP58
 −4.8 TC38235_at Unknown
 −4.86667 TC22191_at Unknown
 −4.95 TC16013_g_at Unknown
 −4.95 TC41433_at Human KIA0436 like
 −5.075 TC32823_at Unknown
 −5.1 TC40705_at Unknown
 −5.175 TC35606_at Unknown
 −5.2 TC33812_at Unknown
 −5.25 TC38211_at EXCM1 gene, regulator SP2 transcription
 −5.25 TC38294_at Unknown
 −5.325 TC34814_at Unknown
 −5.325 TC29508_at Unknown
 −5.4 TC37388_at Transcriptional repressor RP58
 −5.475 TC40986_at Unknown
 −5.55 TC21739_at Unknown
 −5.7 TC41479_at Unknown
 −5.7 TC15800_at Unknown
 −5.7 TC38214_at Unknown
 −5.725 TC16088_at Unknown
 −5.75 TC34430_at Unknown
 −5.825 TC21730_at Unknown
 −5.85 TC25709_g_at Unknown
 −5.675 TC26422_at Unknown
 −6.05 TC28579_at Unknown
 −6.475 TC25709_at Unknown
 −6.675 TC31827_at Unknown
 −6.7 TC16888_at Unknown
 −6.8 TC38692_s_at Unknown
 −8.85 TC35006_at Unknown
 −7.025 TC39106_at Unknown
 −7.675 TC23195_g_at Unknown
 −7.725 TC21739_g_at Unknown
 −7.775 TC39973_at Unknown
 −8.075 TC18151_at Like globulin-7 (zeamayas)
 −8.25 TC32823_g_at Unknown
 −8.475 TC20619_at Similar to alpha/beta hydrolase-1
 −8.675 TC40812_at Unknown
 −8.875 TC20884_at Unknown
 −8.975 TC21031_at Unknown
 −9.225 TC34440_g_at p00071, plakophilin related protein
 −9.25 TC15280_a_at Unknown
 −9.275 TC41038_at Small GTP binding protein
 −9.35 TC31813_at Similar to (highly) GEF protein
 −9.475 TC39216_at HSPC322
 −10.6 TC17986_at Unknown
 −10.6 TC41979_at KIA1424
 −11.275 TC41373_at Unknown
 −11.475 TC18252_at Guanina nucleotide binding protein like
 −12.075 TC15777_at Unknown
 −12.1 TC23934_at RP58, transcriptional repressor
 −12.25 TC42156_at Unknown
 −12.775 TC40806_at Unknown
 −13.075 TC41228_at Unknown
 −13.325 TC32742_at Unknown
 −13.875 TC34340_at Unknown
 −14.075 TC40224_at KIA0898 like
 −14.325 TC17313_at Unknown
 −14.475 TC28738_g_at p53 inducible protein
 −14.525 TC21034_at KIAA0631 like
 −14.575 TC22935_at Unknown
 −15.875 TC30317_g_at VAV-3 protein (GEF protein)
 −15.925 TC39390_at Unknown
 −16.325 TC19908_at Formyltetrahydrofolute dehudrogenase
 −16.05 TC38088_at Unknown
 −19.2 TC16183_at HSPC328
 −19.225 TC40805_at Unknown
 −20.025 TC42007_at Unknown
 −27.3 TC16885_at Angiotensinogen precursor
 −29.425 TC23193_a_at HSPC251
 −33.025 TC26229_at Unknown
 −35.675 TC29945_at Unknown
 −38.65 TC16736_at Unknown
 −45.925 TC19832_a_at Stathmin like protein RB3
 −48.375 TC41060_at Beta 2 chimerin
 −73.95 TC33089_at Unknown
 −76.825 TC29995_at Unknown
 −83.45 TC16446_at Unknown
 −116.975 TC39645_g_at Unknown
 −277.125 TC29990_l_at Unknown
Table 3.
 
Annotated List of Genes with Altered Expression in the Eye Only between Wild-Type and Cln3-Knockout as Compared with the Cerebellum Data Set
Table 3.
 
Annotated List of Genes with Altered Expression in the Eye Only between Wild-Type and Cln3-Knockout as Compared with the Cerebellum Data Set
Change Ratio TIGR/Affymetrix No. Annotation
Upregulated genes
 14.0 TC36735_g_at Unknown
 6.2 TC28305_at Glutaminase C
 4.2 TC25659_at Similar to TRIP protein
 3.4 TC39097_at 42-9-9 protein
 2.7 TC21379_at RhoGAP, GTPase activating protein
Down regulated genes
 −3.0 TC41056_at Unknown
 −3.1 TC14267_i_at RKIP protein
 −3.2 TC32675_s_at MYEF-2
 −3.2 TC17259_g_at Unknown
 −3.4 TC38493_at Unknown
 −3.4 TC40415_at Cytochrome oxidase I
 −3.5 TC30467_at Cytochrome B
 −4.0 TC38290_at NEDF
 −4.1 TC34542_at Ribonucleoprotein A2/B1
 −4.9 TC19304_at ATP Synthase B
 −5.2 TC35606_at Unknown
 −14.5 TC21034_at Lipidosin
 −38.7 TC16736_g_at ELF41A
Figure 2.
 
Validation of gene expression changes by RT-PCR. Expression levels measured by RT-PCR for each sample that was also processed for microarray analysis. Each reaction was repeated in triplicate. Relative expression levels are normalized to GAPDH, which had identical expression in normal and cln3-knockout tissue. Transcripts for glutaminase C and an unknown transcript designated TC36735, which had 6.2- and 14.0-fold increases in expression by microarray analysis, respectively, had a 3.6- and 7.3-fold increase in expression by RT-PCR, respectively. NEDF, lipidosin, and ELF4A, which had respective decreases in expression of −4.0-, −15.5-, −38.7- and −4.9-fold by microarray had decreased expression of −1.9-, −8.0-, −8.3-, and −3.5-fold by RT-PCR, respectively.
Figure 2.
 
Validation of gene expression changes by RT-PCR. Expression levels measured by RT-PCR for each sample that was also processed for microarray analysis. Each reaction was repeated in triplicate. Relative expression levels are normalized to GAPDH, which had identical expression in normal and cln3-knockout tissue. Transcripts for glutaminase C and an unknown transcript designated TC36735, which had 6.2- and 14.0-fold increases in expression by microarray analysis, respectively, had a 3.6- and 7.3-fold increase in expression by RT-PCR, respectively. NEDF, lipidosin, and ELF4A, which had respective decreases in expression of −4.0-, −15.5-, −38.7- and −4.9-fold by microarray had decreased expression of −1.9-, −8.0-, −8.3-, and −3.5-fold by RT-PCR, respectively.
The authors thank Hannah Mitchison (University College of London, London, UK) and Robert Nussbaum (National Human Genome Research Institute) for originally providing the Cln3-knockout mice used to establish the colony of mice for this study. 
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Jarvela I, Sainio M, Rantamaki T, et al. Biosynthesis and intracellular targeting of the CLN3 protein defective in Batten disease. Hum Mol Genet. 1998;7:85–90. [CrossRef] [PubMed]
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Figure 1.
 
(a) Comparison of gross morphologic changes in 10-week-old cln3-knockout and wild-type control mice. Micrographs were taken with a 40× objective and show a representative subsection of the retina with the ganglion cell layer (GCL) on the bottom of the image. (b) Comparison of autofluorescence in 10-week-old cln3-knockout and wild-type control. Photographs were taken with a 40× objective in representative subsection of the retina with the GCL at the bottom of the image. The inner and outer segments of the photoreceptors, which autofluoresce naturally, have been cropped from these images. ONL, outer nuclear layer; OPL, outer plexiform layer; INL, inner nuclear layer; IPL, inner plexiform layer.
Figure 1.
 
(a) Comparison of gross morphologic changes in 10-week-old cln3-knockout and wild-type control mice. Micrographs were taken with a 40× objective and show a representative subsection of the retina with the ganglion cell layer (GCL) on the bottom of the image. (b) Comparison of autofluorescence in 10-week-old cln3-knockout and wild-type control. Photographs were taken with a 40× objective in representative subsection of the retina with the GCL at the bottom of the image. The inner and outer segments of the photoreceptors, which autofluoresce naturally, have been cropped from these images. ONL, outer nuclear layer; OPL, outer plexiform layer; INL, inner nuclear layer; IPL, inner plexiform layer.
Figure 2.
 
Validation of gene expression changes by RT-PCR. Expression levels measured by RT-PCR for each sample that was also processed for microarray analysis. Each reaction was repeated in triplicate. Relative expression levels are normalized to GAPDH, which had identical expression in normal and cln3-knockout tissue. Transcripts for glutaminase C and an unknown transcript designated TC36735, which had 6.2- and 14.0-fold increases in expression by microarray analysis, respectively, had a 3.6- and 7.3-fold increase in expression by RT-PCR, respectively. NEDF, lipidosin, and ELF4A, which had respective decreases in expression of −4.0-, −15.5-, −38.7- and −4.9-fold by microarray had decreased expression of −1.9-, −8.0-, −8.3-, and −3.5-fold by RT-PCR, respectively.
Figure 2.
 
Validation of gene expression changes by RT-PCR. Expression levels measured by RT-PCR for each sample that was also processed for microarray analysis. Each reaction was repeated in triplicate. Relative expression levels are normalized to GAPDH, which had identical expression in normal and cln3-knockout tissue. Transcripts for glutaminase C and an unknown transcript designated TC36735, which had 6.2- and 14.0-fold increases in expression by microarray analysis, respectively, had a 3.6- and 7.3-fold increase in expression by RT-PCR, respectively. NEDF, lipidosin, and ELF4A, which had respective decreases in expression of −4.0-, −15.5-, −38.7- and −4.9-fold by microarray had decreased expression of −1.9-, −8.0-, −8.3-, and −3.5-fold by RT-PCR, respectively.
Table 1.
 
Primers Used for RT-PCR Validation of Expression Levels
Table 1.
 
Primers Used for RT-PCR Validation of Expression Levels
Transcript Primers
GAPDH 5′-GCTCCCTAGGCCCCTCCTG-3′
5′-CAAGAAGGTGGTGAAGCAGGCCAC-3′
Glutaminase C 5′-TAACTGCTAGTATCTGTGCA-3′
5′-AAGAGATAAAGGGTATGTT-3′
Lipidosin 5′-GAAGCTCGGCCTAGAGCGTG-3′
5′-TATGAGCTCCTCCATCGTGT-3′
ELF41A 5′-TTATATGGGAGCAACTTGTC-3′
5′-TTGGTCACTTCTAGCACATC-3′
NEDF 5′-AGTGAAAGATGCAGCCAAGA-3′
5′-ATCGCTCCTGCGGGTTCA-3′
TC36735 5′-GAAACTTGTCTAATACCAG-3′
5′-GACAGTTGTCACCATGAGA-3′
ATP-synthase subunit B 5′-TATGTGCTTGGAACTGGACT-3′
5′-CACTAAGTGGACCTTGATCT-3′
Table 2.
 
Expression Changes Greater Than 2 in Cln3-Knockout Eye, Compared with Wild-Type Control
Table 2.
 
Expression Changes Greater Than 2 in Cln3-Knockout Eye, Compared with Wild-Type Control
Average Change TIGR/Affymetrix No. Annotation
Amino acid metabolism
 22.475 TC39031_at Arginase
 16.925 TC29651_at Possible deaminase
 4.125 TC19442_at Cysteine dioxygenase
 −3.05 TC37346_g_at L-asparaginase
 −4.925 TC28329_g_at NBAT
 −5.325 TC30372_f_at Glutamate dehydrogenase
 −6.15 TC40291_at Tryptophan dioxygenase
 −7.1 TC33164_at Glycine amidotransferase
 −8.375 TC31560_s_at D-aminoacid oxidase
 −20.175 TC24073_at Possible arginine decarboxylase
Blood/vascular
 129.45 TC27670_g_at Myoglobin
 37.075 TC40225_s_at Transthyretin like protein
 23.25 TC32287_at hbr3 brain carboxyesterase
 13.075 TC34069_at Carbonic anhydrase III
 3.425 TC35644_s_at FCK1, VEGF binding, vasculogenisis
 −19.725 TC24493_at Electrogenic Na bicarbonate cotransporter (NBC)
Cell death
 322.8 TC17513_at Death asociated protein DAP1
 158.25 TC37556_at p53 protein
 122.3 TC19787_at p53 apoptosis-associated target
 88.625 TC24816_s_at DAP1 death associated protein
 24.45 TC16227_at Similar to death receptor 6
 20.275 TC15396_at Early quiescence protein-1
 15.825 TC19399_at Apoptosis associated speck protein P(YCARD)
Detox/stress
 32.55 TC40306_f_at Glutathione transferase
 22.85 TC41370_s_at HSP70
 12.2 TC29966_g_at Ceruloplasmin
 4.825 TC35139_at HSBX, heat shock protein, like HSP20
 4.6 TC31120_f_at Plasma glutathione peroxidase
 4.475 TC21222_at Unknown
 −31.325 TC29829_at HSC73
Energy metabolism
 122.7 TC18565_i_at Cytosolic malate dehydrogenase
 48.375 TC15436_s_at Cytochrome c oxidase subunit VIIa-H precursor
 34.575 TC20349_at Creatine kinase
 11.3 TC32389_at PHS1. glycogen phosphorylase
 10.875 TC32884_f_at Lactate dehydrogenase
 7.475 TC23942_i_at Creatine kinase
 6.95 TC19057_g_at Phosphoglycerate mutase muscle-specific subunit
 6.85 TC37832_at Glycogenin-1
 2.825 TC28383_s_at Glucose-6-phosphate dehydrogenase
 −3.425 TC40415_at Cox1, cytochrome oxidase I
 −3.475 TC30467_at NADH dehydrogenase subunit 5
 −4.35 TC38446_g_at Cytochrome oxidase subunit 1
 −4.85 TC19304_at ATP synthase B-subunit
Signaling/Cell Growth
 63.2 TC36530_g_at Mnk2, map kinase interacting kinase
 27.6 TC18256_at Protein kinase Dyrk2
 17.5 TC29599_at TC21 protein
 5.225 TC36530_at Mnk2
 3.825 TC26799_i_at mPRL-3 tyrosine kinase
 3.525 TC34509_g_at MEKK 1, map kinase
 3.275 TC35395_at Caveolin-2
 2.65 TC21379_at RhoGAP, GTPase activating protein
 −2.9 TC21250_g_at Serine/threonine phosphatase 2B
 −2.95 TC25040_at p54, JNK-2, stress activated kinase
 −3.05 TC15005_s_at SHIP2, inositol polyphosphate phosphatase
 −8.1 TC38592_g_at cGMP phosphodiesterase type A9
 −8.5 TC16846_s_at bfgf-r, basic fibroblast growth factor receptor-1
 −9.3 TC15262_at Phosphodiesterase I
 −10 TC34425_g_at fyn(T), tyrosine kinase
 −11.725 TC25522_s_at PCTAIRE-I serine/threonine kinase
 −12.1 TC15645_s_at Inositol 5-phosphatase
 −12.425 TC18155_s_at fyn(T), tyrosine kinase
 −24.65 TC33667_at SPOT14, thyroid hormone inducible protein
 −54.25 TC36931_at Phosphatallic acid phosphotase 2c
Lipid metabolism
 382 TC27653_at 3-ketoacyl-CoA thiolase B
 33.75 TC19057_at Phosphoglycerate mutase muscle-specific subunit
 20.175 TC15810_s_at 3-oxoacyl-CoenzymeA thiolase, mitochondrial
 15.15 TC37551_at Paraoxonase 2 (PON2)
 6.35 TC14864_f_at Keratinocyate lipid-binding protein
 4.85 TC16399_f_at Acyl-CoA dehydrogenase
 4.35 TC33350_at Putative C-8,7 Isomerase
 3.725 TC35242_s_at Heme oxygenase
 −4.875 TC38739_at Diacylglycerol kinase
 −5.05 TC15835_at Oxysterol binding protein
 −5.85 TC37906_s_at Delta-G fatty acid desaturase
 −5.875 TC22730_s_at b-fabp, brain fatty acid binding protein
 −58.775 TC33071_s_at AcylcoA desaturase 2
Protease
 93.35 TC26009_at Stefin 3
 91.05 TC39719_f_at Mac-2, lactose binding lechin
 39.9 TC22206_at CYT4, stefin homolog
 16.8 TC31277_at Serine protease
 14.675 TC35575_at Epithln serine protease
 12.85 TC21695_at Similar to serine proteases
 12.8 TC33498_at Nephrilysin like peptidase
 12.7 TC17364_at Prostasin
 8.275 TC34450_at Aminopeptidase
 7.95 TC34175_at Like aminopeptidase
 6.925 TC16079_at Similar to neurotrypsin
 2.975 TC32493_f_at Cathepsin L
Structural/adhesion/cell surface
 50.9 TC25512_s_at F1SP12 protein, tissue growth factor
 47 TC22866_f_at Collagen alpha-1
 37.85 TC19711_s_at 57 kd keratin
 30.375 TC26960_at Keratin 6 alpha
 28.475 TC30949_at Claudin 7
 26.4 TC24005_s_at Cytokeratin 4
 21.05 TC40219_at VLA-6
 16.75 TC18507_f_at Decorin
 8.825 TC24347_s_at Cytokeratin 13
 8.3 TC33778_i_at Collagen alpha 1
 7.05 TC16852_at Periplakin
 6.825 TC41987_at Desmocollin type 2
 4.9 TC14593_s_at Collagen alpha -2
 4.75 TC40853_f_at Collegan alpha 1
 3.775 TC37852_at Junction adhesion protein
Immune
 137.775 TC23274_at 14-3-3 protein sigma
 132.1 TC20347_at Prostate stem cell antigen
 92.175 TC36394_f_at Galectin-1
 80.725 TC26633_g_at UCP2
 63.725 TC15466_f_at Lipocortin I
 43 TC34607_s_at DBPA homolog
 40.8 TC39759_at TB2 like
 36.2 TC37183_s_at TRP2, dopachrome taulomerase
 33.325 TC40399_s_at Hepatitus virus receptor
 17.8 TC40929_s_at Beta interferon induced protein
 16.575 TC34649_at Similar to IC2
 10.75 TC24304_g_at Linear IgA disease antigen homolog
 8.85 TC25579_at Oncostatin M receptor beta
 7.05 TC14570_f_at C1 inhibitor
 6.425 TC41813_f_at STAT6
 6.275 TC18855_f_at Catpactin 1 light chain
 6.225 TC35184_f_at Macrophage capping protein
 6.2 TC24577_at XLR 4 lymphocyte regulatory protein
 5.925 TC19499_s_at Myc basic motif homologue-1
 5.7 TC24581_at Interferon activatable protein
 4.9 TC28116_g_at DOPAchrome tautomerase
 4.825 TC34110_at LYVE-1, tymphatic endolithium specific receptor
 4 TC15924_at LAR, lenkocyte common anitgen protein
 3.7 TC14368_f_at Lipocortin II / Annexin II (anxII)
 −3.125 TC23291_s_at HUD paraneoplastic antigen
 −3.35 TC36543_at Similar to paraneoplastic antigen, KIAA0883
 −3.7 TC33860_at Neuronal IL-16
 −3.875 TC37323_at Similar to Iga regulatory protein
 −4.1 TC32923_s_at Corticosteroid II-beta dehydrogenase
 −5.15 TC17814_at Corticotropin releasing hormone receptor 2
 −49.575 TC26088_at BM88 antigen
Neuronal cell develepment and function
 294.375 TC32454_at Similar to maxi-K channel
 286.325 TC20337_at Similar to synapsin 1
 75.925 TC16591_at Proleo lipid protein 2
 66.05 TC33406_s_at Peripheral benzodinzepine receptor (ptr)
 64.625 TC30567_s_at Syndecan-1
 60.75 TC36687_at Protein 4.1G
 48 TC19521_g_at Nuclear pore-targeting complex component of 58 kDa
 31.85 TC37537_at Protein 4.1G
 30.1 TC36143_g_at Ezrin
 26.1 TC32955_s_at Els transcription factor
 20.025 TC31586_at Syntaxin 3
 14.575 TC25273_at Dystonin; BPAG-1
 13.225 TC24557_at Dkk-3, dickkopf-3
 12.375 TC30575_at SIX3 protein
 11.1 TC22048_at Semaphorin IV isoform a
 10.45 TC40712_at Connexin 46
 6.625 TC40937_s_at UNC119/ HRG4
 4.125 TC41353_at Glypican 3
 3.725 TC36142_at Ezrin
 3.225 TC41791_at PACSIN2 (syndapin IIaa)
 3.075 TC36827_at Cerebellum postnatal protein-1
 −2.925 TC38522_at KIAA0916 human protein, highwine in drosophila
 −3.05 TC14267_i_at RKIP, phosphoatidylethandlumne binding protein
 −3.175 TC17976_at rsk2, calcium activated K-channel
 −3.2 TC32675_s_at Myelin gene expression factor, myef-2
 −3.225 TC37684_at Kinesin light subunit B, (KLC)
 −3.5 TC26270_s_at KIFI, kinesin like
 −3.525 TC39656_f_at Neuritin
 −3.55 TC41874_at ndr2
 −3.725 TC22759_at Calcineurin b.
 −3.975 TC38290_at Neuroendocrine differentiation factor
 −4.05 TC16990_s_at Neural vision like protein
 −4.275 TC34140_s_at Alpha-catenin (alpha -e)
 −4.3 TC26822_at Acrogranin
 −4.675 TC24292_at ATN2, Na/K transporter subunit 2
 −4.8 TC30767_at SCHIP-1
 −6.325 TC37996_at DARPP-32
 −6.45 TC31890_g_at Secretogranin III
 −7.275 TC39376_at Pro SSAS
 −7.4 TC18154_at Brain development protein BDM1
 −7.8 TC39160_g_at SCG10
 −8.475 TC22283_s_at PLP, myelin proteilipid
 −9.85 TC36359_at TREK-1 K+ channel subunit
 −9.95 TC29998_at Myelin basic protein
 −10.025 TC39061_at Hippocampal amyloid precursor protein (beta)
 −11.65 TC14881_at SCG10
 −13.825 TC24570_at Na/K transporting ATPase, alpha 2 subunit
 −15 TC30390_s_at p21, neuron specific protein
 −16.925 TC18867_at Alpha synuclein
 −18.1 TC39041_at Nel proptein
 −18.9 TC26003_at Synaplogamin XI
 −19.175 TC37308_at Double cortin like protein
 −19.625 TC22741_g_at Neuronal specific septin-3
 −20.625 TC30389_f_at p21, neuron specific protein
 −20.925 TC35356_at Neurilin
 −21.25 TC18648_at NFI-x nucleus factor
 −22.35 TC36040_at Like GCAP1, granule cell marker protein
 −29.375 TC15940_g_at Coat protein gamma cap.
 −48.05 TC22429_s_at Myelin proteolipid protein (PLP)
 −74.375 TC17234_s_at Calbindin
Cytoskeleton factors
 158.975 TC15490_s_at Troponin T fast skeletal muscle isoform
 109.95 TC18963_g_at Beta-tropomyosin
 66.975 TC40898_f_at Troponin 1
 29.275 TC28732_s_at Myosin heavy chain 2a
 19.65 TC19756_at Actin-related protein complex 1b
 15.95 TC22827_at Tropomyosin alpha
 14.325 TC33465_g_at Myosin light chain 1
 13.85 TC15815_at Alpha-actin
 13.725 TC22502_f_at Myosin light chain 2
 12.925 TC28358_f_at Myosin regulatory light chain
 12.5 TC40908_at Tubulin beta 5 subunit
 7.825 TC32100_s_at Alpha actinin -4
 4.025 TC29413_f_at Myosin heavy chain 2B
 3.85 TC39600_f_at Getsolin
 −3.225 TC18165_g_at Prefoldin subunit
 −3.575 TC21995_g_at Microtubule associated protein, tan
 −4.15 TC18613_at Like novel protein c380A1,2.2.
 −4.775 TC20757_s_at ANK-3
 −28.625 TC38163_f_at Tubulin beta-3
unknown
 224.275 TC27018_f_at Gamma 4-crystallin (aa 85-174): gamma-A-crystallin
 121.075 TC27118_at Beta-A4-crystallin
 116.9 TC23815_s_at Mouse fast skeletal muscle SR calcium ATPase
 94.75 TC29087_s_at Unknown
 90.65 TC16275_at Ataxia-telangieclasia group D-associated protein
 86.475 TC15537_f_at Folate-binding protein 1
 79.925 TC23172_at Unknown
 67.825 TC20950_at mCBP
 62.075 TC34763_at Unknown
 57.15 TC16425_s_at Unknown
 52.55 TC18741_f_at Unknown
 44.025 TC37929_at Unknown
 42.8 TC14369_f_at Protein-tyrosine kinase substrate
 39.4 TC16278_at Gamma-C-crystallin
 37.725 TC15584_at Unknown
 36.725 TC32177_at Unknown
 36.725 TC23979_g_at Unknown
 33.5 TC34356_at Unknown
 33.275 TC31887_at Possible glycoprotein
 33.075 TC22352_s_at s100-type calcium binding protein
 32.475 TC26873_at Beta-A3/A1 crystallin
 32 TC30868_f_at PABP polyA binding protein
 31.3 TC31507_at 5100-type calcium binding protein
 29.8 TC36511_at Unknown
 28.275 TC17811_at Unknown
 28.2 TC40393_s_at Calcium binding protein
 27.525 TC41119_at Unknown
 26.875 TC23617_f_at Histone H1
 26.825 TC24011_at Unknown
 26.225 TC27544_at Possible kinase
 25.675 TC20429_at GSG1
 25 TC42144_at Dithiolethiume induced gene
 24.75 TC16184_g_at Unknown
 23.7 TC33945_at Unknown
 23.45 TC30861_at Hepatocellular carcinoma-associated antigen 112
 23 TC37660_s_at Like undine kinase
 21.875 TC37456_at Unknown
 21.8 TC16584_g_at Unknown
 21.3 TC20216_at Unknown
 20.7 TC38463_g_at Onzin
 20.525 TC37769_g_at Unknown
 20 TC38105_at A mannosylglycoprotein b 1–6 acetyl glucosaminyl transferase
 18.2 TC40398_g_at BGP-1 glycoprotein
 17.8 TC39732_at Unknown
 17.65 TC40856_at P8 protein
 16.95 TC22847_s_at Aldose reductase-related protein 1
 16.55 TC22660_at Unknown
 15.825 TC21363_at Unknown
 15.075 TC40330_at Unknown
 14.85 TC37670_g_at Unknown
 14.275 TC21338_at Unknown
 14.075 TC33781_at Unknown
 13.975 TC36735_g_at Unknown
 13.475 TC35151_at Unknown
 13.4 TC37498_g_at Similar to TITIN
 13.35 TC35267_at Unknown
 12.525 TC32779_at Unknown
 12.275 TC22217_g_at Gamma-sarcoglycan
 12.05 TC21382_at Unknown
 11.75 TC38572_at Like KIA0009
 11.225 TC28227_at BM-003
 11.2 TC15010_at Ataxia-telangieclasia group D-associated protein
 10.95 TC40893_f_at Alpha crystallin B-chain
 10.8 TC35947_at Secreted modular calcium binding protein
 10.7 TC42043_s_at Unknown
 10.525 TC35166_at Unknown
 10.35 TC31979_at Unknown
 10.325 TC40743_s_at Transketolase
 10.025 TC24736_at Unknown
 9.8 TC32729_at Unknown
 9.1 TC14992_i_at Double LIM protein-1
 9.05 TC34343_at Unknown
Eye unknown
 8.95 TC31534_g_at RNA binding protein RBP, MS
 8.7 TC37405_at Possible glycoprotein
 8.575 TC34789_at Like echinoderm microtubule associated protein
 8.45 TC41574_g_at Unknown
 8.25 TC40445_at Unknown
 8.1 TC31394_g_at Unknown
 7.425 TC16738_at Cell growth regulating nuclear protein
 7.175 TC35223_g_at Hopotocyte growth factor activator
 6.975 TC19085_f_at Histone H2a 1-F
 6.975 TC19105_g_at Unknown
 6.7 TC16842_at Unknown
 6.675 TC30935_at Unknown
 6.65 TC15420_g_at TGF-beta-inducible protein
 6.625 TC41695_at Unknown
 6.6 TC41312_at Unknown
 6.425 TC36884_at Signal transducer of transcription activator 6
 6.375 TC33908_at Unknown
 6.2 TC28305_at Unknown
 6.175 TC40703_at Unknown
 6.075 TC21210_at Like SIAP-2 sarolemmal associated protein
 6.05 TC22993_s_at Like BM-019
 6.025 TC30968_at Unknown
 5.925 TC38179_at NX-17
 5.75 TC16584_at Unknown
 5.725 TC39835_at Unknown
 5.575 TC31268_at Unknown
 5.575 TC31974_s_at Hapatocyte growth factor activator inhibitor
 5.525 TC35180_at UROPLAKIN IB (UP18)
 5.45 TC34662_g_at FGF binding protein 1
 5.45 TC39762_at Unknown
 5.25 TC22472_g_at Insulin-like growth factor binding protein-4, IGFBP-4
 5.1 TC32825_at Unknown
 5.1 TC15512_at Unknown
 5.05 TC16200_at Unknown
 5.025 TC26659_f_at Gamma E crystallin
 5.025 TC33445_at SM-20, growth factor responsive protein
 5 TC31101_g_at NX-17
 4.95 TC32986_g_at SGLT1 sodium glucose transporter-1
 4.925 TC28395_at Unknown
 4.75 TC39257_g_at Unknown
 4.75 TC41820_f_at pnbp1, poly a binding protein
 4.725 TC33957_f_at Unknown
 4.7 TC16337 s at Aldose reductase-related protein 1 reductase
 4.7 TC38699_at Unknown
 4.55 TC39978_at Unknown
 4.475 TC23656_g_at HSP 70
 4.45 TC16809_at Sialomucin MGC-24
 4.425 TC34081_at Unknown
 4.275 TC32695_a_at TtSII B
 4.15 TC25859_at Unknown
 4.025 TC34228_g_at Unknown
 4 TC40849_at KIAA 1561 like
 3.775 TC36904_g_at Unknown
 3.775 TC41912_at Unknown
 3.725 TC41574_at Unknown
 3.7 TC33236_f_at Collagen alpha-2
 3.675 TC38758_at Similar to ribonuclease
 3.65 TC40553_at Predicted osteoblast protein G53786
 3.525 TC16880_at Unknown
 3.5 TC41930_at ZNT4 zinc transporter 4
 3.425 TC18373_at Unknown
 3.425 TC36701_at MEA1 antigen
 3.425 TC37498_at Like title
 3.4 TC33329_at Cavaolio-1
 3.35 TC28712_at Unknown
 3.325 TC26918_i_at Ocant-binding transcription factor I (cbta)
 3.275 TC35003_s_at Initiation factor
 3.25 TC17314_at Unknown
 3.175 TC28860_at Unknown
 3.175 TC28860_at Unknown
 3.15 TC30867_at PAB1, polyadcnytate binding protein
 3.125 TC34228_at Unknown
 3.1 TC33264_at Guanine nucleotide binding protein
 2.925 TC22848_s_at UBC3
 2.9 TC28660_g_at Unknown
 2.7 TC34620_f_at Ribosomal protein 520
 −2.8 TC14392_f_at Stathmin
 −2.85 TC18861_at Unknown
 −2.85 TC24550_at Unknown
 −2.925 TC39474_f_at Lactate dehydrogynase
 −2.975 TC33078_at Unknown
 −3 TC41056_at Unknown
 −3.125 TC32289_a_at ABC2
 −3.175 TC18736_g_at Protein synthesis initiation factor 4A, ELF41A
 −3.175 TC29636_at Unknown
 −3.175 TC41293_at Unknown
 −3.2 TC41345_at Unknown
 −3.225 TC17259_g_at Unknown
 −3.225 TC20592_at Small nuclear ribonucleo protein, SmO
 −3.25 TC34446_at Unknown
 −3.275 TC16825_at Unknown
 −3.275 TC24812_at Unknown
 −3.3 TC39752_at Unknown
 −3.3 TC40014_at Unknown
 −3.35 TC25091_at Transcription repressor RPS8
 −3.35 TC38493_at Unknown
 −3.35 TC22066_at Unknown
 −3.4 TC33205_at SERCA 2n
 −3.425 TC28327_at Similar to EXTL2 human
 −3.5 TC15898_f_at Similar to LDOC1 human
 −3.5 TC22782_g_at Similar to cadherin 22
 −3.525 TC22801_at PAK-1 threoniae/serine kinase p21 activated
 −3.575 TC35044_at Unknown
 −3.65 TC25610_s_at Neodin
 −3.7 TC37065_at Same as FCJ10856 human protein
 −3.875 TC27925_i_at Plallet activating factor PAF acatythydroinse
 −3.95 TC29662_at Unknown
 −3.975 TC22817_at Brain protein 154
 −4.05 TC38604_at Unknown
 −4.075 TC18152_at Unknown
 −4.075 TC38584_at KIA1583 human protein
 −4.125 TC34542_at Ribonucleoprotein A2/B1
 −4.15 TC19732_at Unknown
 −4.3 TC33029_g_at Unknown
 −4.3 TC37489_a_at Mouse brain protein, BH5, peanut-like
 −4.475 TC39750_at Unknown
 −4.525 TC39858_at Unknown
 −4.55 TC34778_at Unknown
 −4.575 TC38646_at KIA0436, human, like oligopeptidase
 −4.6 TC26109_at Unknown
 −4.6 TC36755_at Neural membrane glyco protein, M6–8
 −4.7 TC39581_at Unknown
 −4.725 TC22193_at Transcriptional repressor RP58
 −4.8 TC38235_at Unknown
 −4.86667 TC22191_at Unknown
 −4.95 TC16013_g_at Unknown
 −4.95 TC41433_at Human KIA0436 like
 −5.075 TC32823_at Unknown
 −5.1 TC40705_at Unknown
 −5.175 TC35606_at Unknown
 −5.2 TC33812_at Unknown
 −5.25 TC38211_at EXCM1 gene, regulator SP2 transcription
 −5.25 TC38294_at Unknown
 −5.325 TC34814_at Unknown
 −5.325 TC29508_at Unknown
 −5.4 TC37388_at Transcriptional repressor RP58
 −5.475 TC40986_at Unknown
 −5.55 TC21739_at Unknown
 −5.7 TC41479_at Unknown
 −5.7 TC15800_at Unknown
 −5.7 TC38214_at Unknown
 −5.725 TC16088_at Unknown
 −5.75 TC34430_at Unknown
 −5.825 TC21730_at Unknown
 −5.85 TC25709_g_at Unknown
 −5.675 TC26422_at Unknown
 −6.05 TC28579_at Unknown
 −6.475 TC25709_at Unknown
 −6.675 TC31827_at Unknown
 −6.7 TC16888_at Unknown
 −6.8 TC38692_s_at Unknown
 −8.85 TC35006_at Unknown
 −7.025 TC39106_at Unknown
 −7.675 TC23195_g_at Unknown
 −7.725 TC21739_g_at Unknown
 −7.775 TC39973_at Unknown
 −8.075 TC18151_at Like globulin-7 (zeamayas)
 −8.25 TC32823_g_at Unknown
 −8.475 TC20619_at Similar to alpha/beta hydrolase-1
 −8.675 TC40812_at Unknown
 −8.875 TC20884_at Unknown
 −8.975 TC21031_at Unknown
 −9.225 TC34440_g_at p00071, plakophilin related protein
 −9.25 TC15280_a_at Unknown
 −9.275 TC41038_at Small GTP binding protein
 −9.35 TC31813_at Similar to (highly) GEF protein
 −9.475 TC39216_at HSPC322
 −10.6 TC17986_at Unknown
 −10.6 TC41979_at KIA1424
 −11.275 TC41373_at Unknown
 −11.475 TC18252_at Guanina nucleotide binding protein like
 −12.075 TC15777_at Unknown
 −12.1 TC23934_at RP58, transcriptional repressor
 −12.25 TC42156_at Unknown
 −12.775 TC40806_at Unknown
 −13.075 TC41228_at Unknown
 −13.325 TC32742_at Unknown
 −13.875 TC34340_at Unknown
 −14.075 TC40224_at KIA0898 like
 −14.325 TC17313_at Unknown
 −14.475 TC28738_g_at p53 inducible protein
 −14.525 TC21034_at KIAA0631 like
 −14.575 TC22935_at Unknown
 −15.875 TC30317_g_at VAV-3 protein (GEF protein)
 −15.925 TC39390_at Unknown
 −16.325 TC19908_at Formyltetrahydrofolute dehudrogenase
 −16.05 TC38088_at Unknown
 −19.2 TC16183_at HSPC328
 −19.225 TC40805_at Unknown
 −20.025 TC42007_at Unknown
 −27.3 TC16885_at Angiotensinogen precursor
 −29.425 TC23193_a_at HSPC251
 −33.025 TC26229_at Unknown
 −35.675 TC29945_at Unknown
 −38.65 TC16736_at Unknown
 −45.925 TC19832_a_at Stathmin like protein RB3
 −48.375 TC41060_at Beta 2 chimerin
 −73.95 TC33089_at Unknown
 −76.825 TC29995_at Unknown
 −83.45 TC16446_at Unknown
 −116.975 TC39645_g_at Unknown
 −277.125 TC29990_l_at Unknown
Table 3.
 
Annotated List of Genes with Altered Expression in the Eye Only between Wild-Type and Cln3-Knockout as Compared with the Cerebellum Data Set
Table 3.
 
Annotated List of Genes with Altered Expression in the Eye Only between Wild-Type and Cln3-Knockout as Compared with the Cerebellum Data Set
Change Ratio TIGR/Affymetrix No. Annotation
Upregulated genes
 14.0 TC36735_g_at Unknown
 6.2 TC28305_at Glutaminase C
 4.2 TC25659_at Similar to TRIP protein
 3.4 TC39097_at 42-9-9 protein
 2.7 TC21379_at RhoGAP, GTPase activating protein
Down regulated genes
 −3.0 TC41056_at Unknown
 −3.1 TC14267_i_at RKIP protein
 −3.2 TC32675_s_at MYEF-2
 −3.2 TC17259_g_at Unknown
 −3.4 TC38493_at Unknown
 −3.4 TC40415_at Cytochrome oxidase I
 −3.5 TC30467_at Cytochrome B
 −4.0 TC38290_at NEDF
 −4.1 TC34542_at Ribonucleoprotein A2/B1
 −4.9 TC19304_at ATP Synthase B
 −5.2 TC35606_at Unknown
 −14.5 TC21034_at Lipidosin
 −38.7 TC16736_g_at ELF41A
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