GEO DataSets

Analysis of lens from ICR embryos at 3 key developmental stages in the transition from E10.5 lens placode invagination to E12.5 lens primary fiber cell differentiation and matched whole embryo body (WB, minus ocular tissue) controls. Results provide insight into molecular basis of lens development.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 4 development stage, 2 tissue sets

Platform:

GPL1261

Series:

GSE32334

13 Samples

Download data: CEL

(Submitter supplied) Identification of genes involved in ocular birth defects remains a challenge. To facilitate the identification of genes associated with cataract, we developed iSyTE (integrated Systems Tool for Eye gene discovery; http://bioinformatics.udel.edu/Research/iSyTE). iSyTE contains microarray gene expression profiles of the mouse embryonic lens as it transitions from the stage of placode invagination to that of vesicle formation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Datasets:

GDS4452 GDS4453

Platform:

GPL1261

19 Samples

Download data: CEL

Analysis of laser capture microdissected tooth germ tissue from ICR E13.5 embryos and matched whole embryo body (WB, without tooth germ) controls representing stages E11.5, E12.5, and E13.5. Results provide insight into molecular mechanisms underlying tooth development.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 development stage, 2 tissue sets

Platform:

GPL1261

Series:

GSE32334

6 Samples

Download data: CEL

(Submitter supplied) We applied previously established in silico whole-embryo body (WB)-subtraction-based approach to identify “lens-enriched” genes. These new RNA-seq datasets on embryonic stages E10.5, E12.5, E14.5 and E16.5 confirmed high expression of established cataract-linked genes and identified several new potential regulators in the lens. Finally, we present lens stage-specific UCSC Genome Brower annotation-tracks; these are publicly accessible through iSyTE (https://research.bioinformatics.udel.edu/iSyTE/) and enable a user-friendly visualization of lens gene expression/enrichment to help prioritize genes from high-throughput data from cataract cases.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

15 Samples

Download data: TXT

(Submitter supplied) Purpose: While the bioinformatics gene-discovery tool iSyTE (integrated Systems Tool for Eye gene discovery) has proved effective in identifying new cataract-linked genes, it primarily depended on lens-enriched expression of just three wild-type mouse embryonic stages. To increase iSyTE’s efficacy, a broad range of embryonic (E) and postnatal (P) lens microarray datasets from wild-type and specific gene-perturbation mutant mice were analyzed and a new web-interface was developed for their effective access and downstream-analysis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

12 Samples

Download data: TXT

(Submitter supplied) Although majority of the genes linked to pediatric cataract exhibit lens fiber cell-enriched expression, our understanding of gene regulation in these cells is limited to function of just eight transcription factors and largely in the context of crystallins. Here, we identify small Maf transcription factors MafG and MafK as regulators of several non-crystallin human cataract genes in fiber cells and establish their significance to cataract. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

4 Samples

Download data: TXT

(Submitter supplied) Celf1 germline or conditional deletion mouse mutants exhibit fully penetrant lens defects including cataract. To gain insight into gene expression changes underlying these lens defects Differential Gene Expression analysis was performed for lenses obtained from control and Celf1 conditional deletion mutant mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: CSV

(Submitter supplied) Celf1 germline or conditional deletion mouse mutants exhibit fully penetrant lens defects including cataract. To gain insight into gene expression changes underlying these lens defects, microarray comparison was performed for lenses obtained from control and Celf1 conditional deletion mutant mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

4 Samples

Download data: CSV

(Submitter supplied) Mutations/deficiency of TDRD7, which encodes a tudor domain containing protein involved in post-transcriptional gene expression control, causes early-onset cataract in humans and animal models. While Tdrd7 is implicated in the control of key lens mRNAs, the impact of Tdrd7 deficiency on microRNAs (miRNAs), and how this contributes to cataracts, is undefined. Here, we address this critical knowledge-gap by investigating Tdrd7-targeted knockout (Tdrd7-/-) mice that exhibit fully penetrant juvenile cataracts. more...

Organism:

synthetic construct; Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL16384

6 Samples

Download data: CEL

(Submitter supplied) Mutations of the RNA-granule component TDRD7 (OMIM: 611258) cause pediatric cataract in humans. Here, we applied an integrated approach to elucidate the molecular pathology of cataract in Tdrd7 targeted-knockout (Tdrd7-/-) mice. Tdrd7-/- animals precipitously develop lens fiber cell abnormalities early in life, suggesting a global-level breakdown/mis-regulation of key cellular processes. High-throughput RNA-sequencing followed by iSyTE-integrated bioinformatics-based analysis identified the molecular chaperone and cytoskeletal-modulator, HSPB1 (HSP27), among the high-priority down-regulated candidates in Tdrd7-/- lens. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

18 Samples

Download data

(Submitter supplied) Analysis of Tdrd7 deficiency in mouse lens epithelial-derived cell line at gene expression level. The hypothesis tested was that Tdrd7 is involved in post-transcriptional control of gene expression in the lens. Results provide evidence for differential regulation of genes involved in lens homeostasis and cataract formation in the absence of Tdrd7. In eukaryotic cells, cytoplasmic RNA granules (RGs) function in the post-transcriptional control of gene expression. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

(Submitter supplied) Purpose: Transcriptome is the entire repertoire of all transcripts present in a cell at any particular time. We undertook next-generation whole transcriptome sequencing approach to gain insight of the transcriptional landscape of the developing mouse lens. Methods: We ascertained mice lenses at six developmental time points including two embryonic (E15 and E18) and four postnatal stages (P0, P3, P6, and P9). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

24 Samples

Download data: XLSX

(Submitter supplied) We performed RNA-seq with both wild type and N-myc knock-out E14 mouse lenses and identified the differentially expressed genes affected by N-myc knockout.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

5 Samples

Download data: TXT

(Submitter supplied) The objective of the present study was to use our own fabricated bovine embryo cDNA microarray to profile genome-wide expression patterns of genes during the implantation period. Duplicate readings were obtained by hybridization of a Cy3/Cy5 probe mixture for each sample. Data normalization was performed the local background intensity of each array spot was smoothed by the local weight regression (lowess) smoother and subtracted from spot intensity data. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Dataset:

GDS1003

Platform:

GPL1221

11 Samples

Download data: TIFF

Expression profiling of embryos at various days of gestation up to 21 days and fetuses and fetal membranes at 27 and 28 days of gestation. Results provide insight into the regulation of embryonic, fetal, and fetal membrane differentiation.

Organism:

Bos taurus

Type:

Expression profiling by array, count, 7 development stage, 3 tissue sets

Platform:

GPL1221

Series:

GSE1414

11 Samples

Download data: TIFF

(Submitter supplied) Prolonged use of glucocorticoids can lead to the formation of a cataract, however the mechanism is not known. We recently reported the presence of the functional glucocorticoid receptor in immortalized cultured mammalian lens epithelial cells (Gupta & Wagner, Invest Ophthalmol Vis Sci 2003), but the short term biological effect of glucocorticoid action in lens epithelial cells is not known. This study seeks to examine glucocorticoid induced changes in global gene expression in LECs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1353

Platform:

GPL96

12 Samples

Download data

Analysis of cultured immortalized lens epithelial cells (LEC) 4 and 16 hours after treatment with 1 uM dexamethasone, a glucocorticoid steroid hormone. Long-term glucocorticoid use can induce cataract formation. Results identify glucocorticoid targets and short-term effects of glucocorticoid on LECs

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 agent, 2 time sets

Platform:

GPL96

Series:

GSE3040

12 Samples

Download data

(Submitter supplied) The Shumiya cataract rat (SCR) is a model for hereditary cataract. Two-third of these rats develop lens opacity within 10-11-weeks. Onset of cataract is attributed to the synergetic effect of lanosterol synthase (Lss) and farnesyl-diphosphate farnesyltransferase 1 (Fdft1) mutant alleles that lead to cholesterol deficiency in the lenses, which in turn adversely affects lens biology including the growth and differentiation of lens epithelial cells (LECs). more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL17117

2 Samples

Download data: CEL

(Submitter supplied) Notch signaling is essential for proper lens development, however the specific requirements of individual Notch receptors has not been previously investigated. Here we report the lens phenotypes of Notch2 conditionally mutant mice, which exhibited severe microphthalmia, reduced pupillary openings, disrupted fiber cell morphology, eventual loss of the anterior epithelium, fiber cell dysgenesis, and cataracts. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL