Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of retina from 6 pairs of litter-matched Bhlhe23-/- and wild type mice at postnatal day 7

ABSTRACT: Bhlhe23 is a transcription factor that is required for the maturation and survival of retinal rod bipolar cells in mice. In the Bhlhe23-/- retina, rod bipolar cells are born in normal numbers, then die by apoptosis from postnatal day 8. We identified genes that were likely to be important to rod bipolar cell development and survival by identifying genes that were significantly differentially expressed in the transcriptome of the Bhlhe23-/- mouse retina compared with wild type retina at postnatal day 7. just before the onset of rob bipolar cell death.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Sasha Woods

PROVIDER: E-MTAB-6071 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparison of the retinal transcriptomes of four Bhlhe23-/- mice and 4 sex and litter-matched wild type mice

Project description:Bhlhe23 is a transcription factor that is required for the maturation and survival of retinal rod bipolar cells in mice. In the adult Bhlhe23-/- retina, rod bipolar cells are almost completely absent. We identified genes that were likely to be important to rod bipolar cell maintenance and function by identifying genes that were significantly down-regulated in the transcriptome of adult Bhlhe23-/- mouse retina compared with wild type retina.

2017-09-20 | E-MTAB-6069 | biostudies-arrayexpress

Single cell RNA-seq of adult human neural retina

Project description:To comprehensively profile cell types in the human retina, we performed single cell RNA-sequencing on 20,009 cells obtained post-mortem from three donors and compiled a reference transcriptome atlas. Using unsupervised clustering analysis, we identified 18 transcriptionally distinct clusters representing all known retinal cells: rod photoreceptors, cone photoreceptors, Müller glia cells, bipolar cells, amacrine cells, retinal ganglion cells, horizontal cells, retinal astrocytes and microglia.

2019-08-21 | E-MTAB-7316 | biostudies-arrayexpress

Transcription profiling of Gata3 conditional knock out mice to investigate epidermis and hair follicle differentiation

Project description:Transcriptome analysis on Gata3 conditional knock out murine hair follicles. Background. The transcription factor Gata3 is critically involved in epidermis and hair follicle differentiation. Yet, little is known about how Gata3 co-ordinates stem cell lineage determination in skin, which processes are mostly implicated and how Gata3 differentially regulates distinct cell populations within the hair follicle. Here, we describe a conditional Gata3-/- mouse (K14-Gata3-/-) in which Gata3 is specifically deleted in epidermis and hair follicles. Principal findings. K14-Gata3-/- mice show aberrant postnatal growth and development, delayed hair growth and maintenance, abnormal hair follicle organization and irregular pigmentation. After the first hair cycle, the germinative layer surrounding the dermal papilla was not restored; instead, proliferation was pronounced in basal epidermal cells. Transcriptome analysis of laser-dissected K14-Gata3-/- hair follicles as compared to wild type littermate controls, revealed mitosis, epithelial differentiation and the Notch, WNT and BMP signalling pathways to comprise significantly overrepresented processes. Conclusions. Subsequent elucidation of these pathways at the RNA and protein levels and physiologic endpoints shows that Gata3 integrates diverse signalling networks to regulate the balance between hair follicle and epidermal cell fates.

2007-01-01 | E-MEXP-634 | biostudies-arrayexpress

Circadian and light-driven regulation of rod dark adaptation

Project description:The sensation of light is initiated in photoreceptor cells by the photoisomerization of a chromophore molecule from 11-cis to all-trans retinal. Continuous visual perception requires recycling of the spent chromophore back to the 11-cis form through the visual cycle, a series of reactions in the retinal pigmented epithelium (RPE). Light-driven chromophore consumption by photoreceptors is greater in daytime compared to night time, suggesting that correspondingly higher activity of the visual cycle may be required. On the other hand, as rod photoreceptors are saturated in bright light, the continuous turnover of their chromophore through the visual cycle during daytime would unnecessarily utilize precious energy and produce toxic byproducts. Here, we sought to determine whether the recycling of chromophore and the dark adaptation of rods is regulated by the circadian clock and light exposure. We demonstrate that in melatonin-proficient C3H/f+/+ mice, rod dark adaptation is slower during the day or after light exposure. This surprising daytime downregulation of the RPE visual cycle was further demonstrated by gene analysis, which revealed light-driven reduction in the expression of Rpe65, which encodes a key enzyme of the RPE visual cycle. In contrast, rods in melatonin-deficient strains (C57BL6/J and 129/Sv) were not affected by this daily visual cycle modulation. Our results demonstrate that the circadian clock and light exposure regulate the recycling of chromophore in the RPE visual cycle. This daily modulation of rod dark adaptation is mediated by melatonin and could potentially protect the retina from light-induced damage during the day. mRNA-seq of murine eyes (lens removed) in objective day (OD) vs. subjective day (SD) conditions (2 biological replicates per condition). Each biological replicate consisted of 4 eyes (from 1 female and 1 male).

2015-11-19 | E-GEOD-68470 | biostudies-arrayexpress

A role for Prenylated rab acceptor 1 in vertebrate photoreceptor development

Project description:The rd1 mouse retina is a well-studied model of retinal degeneration where rod photoreceptors undergo cell death beginning at postnatal day P10 until P21. This period coincides with photoreceptor terminal differentiation in a normal retina. We have used the rd1 retina as a model to investigate early molecular defects in developing rod photoreceptors prior to the onset of degeneration. Using a microarray approach, we performed gene profiling comparing rd1 and wild type retinas at four time points starting at P2, prior to any obvious biochemical or morphological differences, and concluding at P8, prior to the initiation of cell death. We have identified genes that are differentially regulated in the rd1 retina at early time points, which may give insights into developmental defects that precede photoreceptor cell death. This is the first report of PRA1 expression in the retina. Our data support the hypothesis that PRA1 plays an important role in vesicular trafficking between the Golgi and cilia in differentiating and mature rod photoreceptors. Retinal samples were harvested from both rd1/le and wt animals at postnatal days 2, 4, 6, and 8 for microarray. Each sample included 8-14 retinas and experiments were performed in quadruplicate. Ten micrograms of total RNA was used for cDNA systhesis in target molecule production.

2012-11-02 | E-GEOD-41821 | biostudies-arrayexpress

Transcription profiling of mouse retina from four genotypes: +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl at P14 and P28

Project description:Rorb is essential for rod photoreceptor development in the mouse retina. Using Affymetrix mouse GeneChips, we have generated expression profiles of the +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl retina at P14 and P28. In this dataset, we include the expression data obtained from retina of wt and mutants. These data are used to obtain 1189 genes that are differentially expressed in Rorb-/- vs wt. Experiment Overall Design: 31 total samples were analyzed

2009-10-23 | E-GEOD-16585 | biostudies-arrayexpress

The proteome of normal human retina

Project description:The retina is a delicate tissue that detects light, converts photochemical energy into neural signals, and transmits the signals to the visual cortex of the brain. A detailed protein inventory of the proteome of the normal human eye may provide a foundation for new investigations into both the physiology of the retina and the pathophysiology of retinal diseases. To provide an inventory, proteins were extracted from five retinas of normal eyes and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed in duplicate using LC-MS/MS on an Orbitrap Elite mass spectrometer. A total of 3,436 non-redundant proteins were identified in the human retina, including 20 unambiguous protein isoforms, of which 8 have not previously been demonstrated to exist at the protein level. The proteins identified in the retina included most of the enzymes involved in the visual cycle and retinoid metabolism. One hundred and fifty-eight proteins that have been associated with age-related macular degeneration were identified in the retina. The MS proteome database of the human retina may serve as a valuable resource for future investigations of retinal biology and disease.

2014-11-27 | PXD001242 | Pride

KK_Arhgap28

Project description:Microarray comparison of gene expression between bone tissues of wild type and Arhga28del mice

2015-01-08 | E-MTAB-2296 | biostudies-arrayexpress

Transcription profiling of chicken retinal gene expression during imposed myopic defocus

Project description:The retina plays an important regulatory role in ocular growth. To screen for new retinal candidate genes that could be involved in the inhibition of ocular growth, we used chick microarrays to analyze the changes in retinal mRNA expression after myopic defocus was imposed by positive lens-wear. Chicks were raised under a 12h-light/12h-dark cycle (light-onset: 8:00 am and light-offset: 8:00 pm) with unrestricted access to water and food. On the day prior to the experiment, velcro rings were glued to the feathers around the eye under diethylether anaesthesia. Four male white leghorn chicks, aged 9 days, wore +6.9D spectacle lenses over both eyes for 24 hours. Four untreated age-matched male chicks from the same batch served as controls. After decapitation of the chicks, the eyes were enucleated and the retina was prepared. The retinae from both eyes of each chick were pooled for RNA isolation. Experiment Overall Design: Four samples each: Retina of both eyes of +6.9 diopter lens-treated chicks (plus_lens), Retina of both eyes of untreated control chicks (control)

2008-11-04 | E-GEOD-11439 | biostudies-arrayexpress

Gene expression data in the retina in HIV positive and HIV negative eyes

Project description:To examine the gene expression data in the retina in HIV positive and HIV negative autopsy eyes we used a microarray approach with the HumanHT-12 v4 Expression BeadChip. Retinal punches were made for the following regions CWS = cotton wool spot IRH = intra-retinal hemorrhage PP = posterior pole

2013-09-20 | E-MEXP-3757 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data