GEO DataSets

(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) 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) 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) 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 experiment is aimed to compare the transcriptomes of rbm24a mutant and wildtype at 33 hpf. As Rbm24a is an RNA binding protein, this comparation is suitable to obtain information on differential gene expression and alternative splicing. We found that the expression of most of the crystallin genes and many other lens specific genes are down regulated in rbm24a mutant, without changes in splicing patterns.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: XLS, XLSX

(Submitter supplied) This experiment is aimed to compare the transcriptomes of rbm24a mutant and wildtype at 33 hpf. As Rbm24a is an RNA binding protein, this comparation is suitable to obtain information on differential gene expression and alternative splicing. We found that the expression of most of the crystallin genes and many other lens specific genes are down regulated in rbm24a mutant, without changes in splicing patterns.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

2 Samples

Download data: XLS

(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:

Mus musculus; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL16384

6 Samples

Download data: CEL

(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 report systematical profiling of translation efficiency in stress conditions of NIH3T3 cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19057

8 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) In cell stress, mRNA in the cytoplasm is sequestered to the insoluble ribonucleoprotein (RNP) compartments containing stress granules. These RNP granules are known to be involved in the control of mRNA processing and decay, but it has been elusive whether the mRNA redistribution in cell stress is universal or specific to a subset of transcripts. Here we provide a transcriptome-wide profiles of the RNP granules in cell stress and show that mRNA accumulation in stress granule differentially affects individual  transcripts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

24 Samples

Download data: TXT

(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) To investigate the relationship between histones, chaperone function, and cataracts, we performed RNA-seq, isothermal titration calorimetry (ITC), size-exclusion chromatography, and gel electrophoresis of histones. The RNA-seq of postnatal lenses from 2-day-old cryaa -R49C  mice revealed increased histone gene expression, suggesting that a α-crystallin mutation regulates histones via a transcriptional mechanism .

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: TXT

(Submitter supplied) The transcription factor Pax6 is comprised of the paired domain (PD) and homeodomain (HD). In the developing forebrain, Pax6 is expressed in ventricular zone precursor cells and in specific subpopulations of neurons; absence of Pax6 results in disrupted cell proliferation and cell fate specification. Pax6 also regulates the entire lens developmental program. To reconstruct Pax6-dependent gene regulatory networks (GRNs), ChIP-seq studies were performed using lens and forebrain chromatin from mice. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL11002 GPL17021

24 Samples

Download data: BED, NARROWPEAK, TXT