GEO DataSets

(Submitter supplied) The cerebral cortex plays an important role in cognitive function and specialized perception in mammals and its development requires highly specific spatio-temporal control of gene expression. The study identified stage- and region-specific markers throughout cerebral corticogenesis at various important stages of cerebral cortex development; embryonic day (E) 15.5, E17.5, postnatal day (P) 1.5 and 4-6 months old.

Organism:

Mus musculus

Type:

Expression profiling by SAGE

Platforms:

GPL1349 GPL11

12 Samples

Download data

(Submitter supplied) We sought to find molecular signatures of the SGZ cell types, and to characterize the molecular pathways and transcription factor cascades that define the neurogenic niche. We used laser capture microdissection and DNA microarrays to profile gene expression in the inner (SGZ) and outer portions of the dentate gyrus (DG). Since the vast majority of the cells in the DG are mature granule cells, we compared the expression of the inner and outer portions to reveal molecular markers for the less numerous populations of the SGZ. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5005

Platform:

GPL81

18 Samples

Download data: CEL

Analysis of LCM samples of the subgranular zone (SGZ) of the hippocampal dentate gyrus isolated from adults subjected to running for up to 30 days. The SGZ is a major site of neurogenesis in adult brain. Running enhances SGZ proliferation. Results provide insight into the SGZ molecular environment.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 cell type, 9 individual, 2 protocol, 3 time sets

Platform:

GPL81

Series:

GSE39697

18 Samples

Download data: CEL

(Submitter supplied) Many neurological and psychiatric disorders affect the cerebral cortex, and a clearer understanding of the molecular processes underlying human corticogenesis will provide greater insight into such pathologies. To date, knowledge of gene expression changes accompanying corticogenesis is largely based on murine data. Here we present a searchable, comprehensive, temporal gene expression dataset encompassing cerebral cortical development from human embryonic stem cells (hESCs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

44 Samples

Download data: CSV

(Submitter supplied) The genes regulated by SOX11 in MCL was investigated in MCL cell line Granta 519 by siRNA knock down system. Cells were transfected using the LONZA electroporation system. Results represent cells harvested after 20 hours. Details of the experiment is published in PMID 21124928.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

12 Samples

Download data: CEL, TXT

(Submitter supplied) Transcriptional profiling of Sox4cKO, Sox11cKO, or Sox4/11dcKO mouse keratinocytes as compared to their wild-type control keratinocytes, isolated from gender matched neonatal pairs. Goal was to identify the genes differentially expresssed in the conditional knockout keratinocytes vs the wild-type control.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

6 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of mouse E16 epidermis deficient of Sox4, Sox11, or both as compared to gender matched wild type littermate controls. Goal was to identify the genes differentially expresssed in the conditional knockout epidermis vs the wild-type control epidermis.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

6 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of SOX11-expressing mouse epidermis (K14-rtTA;TRE-Sox11-FLAG) compared to control (K14-rtTA) epidermis at postnatal day 4 (P4). The littermate pairs were injected with Dox for 12 h before their epidermis was harvested. Goal was to identify the gene expression profile of postnatal epidermis changed by SOX11 induced expression.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

2 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of mouse epidermal cells at embryonic day 13 (E13) compared with epidermal basal cells at postnatal day 4 (P4), both isolated from Krt14-H2BGFP mouse skin. Goal was to identify the genes differentially expresssed in E13 epidermal cells vs P4 epidermal basal cells.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

2 Samples

Download data: TXT

(Submitter supplied) Tissue injury induces changes in cellular identity, but the underlying molecular mechanisms remain obscure. Here, we show that upon damage, epidermal cells at the wound edge convert to an embryonic-like state, altering particularly the cytoskeletal/extracellular matrix (ECM) components and differentiation program. We show that SOX11 and its closest relative SOX4 dictate embryonic epidermal state, regulating genes involved in epidermal development as well as cytoskeletal/ECM organization. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

5 Samples

Download data: BEDGRAPH, TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL13112

57 Samples

Download data: TXT

(Submitter supplied) In vitro cortex generated from embryonic stem cells (ESCs) is a model system to investigate corticogenesis and a promising tool for cortical therapy. A fundamental question that has implications for understanding corticogenesis and for using stem cells therapeutically is to determine whether in vitro cortex reproduces some fine-tuned epigenetic modifications that are important for corticogenesis and function in vivo such as parent-of-origin dependent DNA methylation and expression of imprinted genes (IGs). more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

26 Samples

Download data: TXT

(Submitter supplied) In vitro differentiation of embryonic stem cells (ESC) provides models that reproduce in vivo development and cells for therapy. Whether the epigenetic signatures that are crucial for brain development and function and that are sensitive to in vitro culture are similar between native brain tissues and their artificial counterpart generated from ESC is largely unknown. Here, using RNA-seq we have compared the parental origin-dependent expression of imprinted genes (IGs), a model of epigenetic regulation, in cerebral cortex generated either in vivo, or from ESCs using in vitro corticogenesis, a model that reproduces the landmarks of in vivo corticogenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

31 Samples

Download data: TXT, XLS

(Submitter supplied) Although there have been studies conducted on cornea and retina growth and development, postnatal gene expression studies on sclera growth during postnatal growth has not been well characterised. Given that the mouse genome has 85% homology to the human genome and has been completely sequenced, mouse model for the study of ocular growth has advantages over other animal models. Thus, we aimed to study the biology and genetics behind sclera growth during post-natal development in Balb/cJ mice as a means to understand genetic changes that cause scleral growth and development during post-natal eye development The purpose of this study was to identify the genes underlying the development of mouse sclera post-natal growth of the posterior chamber of the eye using microarray

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

30 Samples

Download data: CEL

(Submitter supplied) During organogenesis, neural and mesenchymal progenitor cells give rise to many cell lineages, but their molecular requirements for self-renewal and lineage decisions are incompletely understood. Here we show that their survival critically relies on the redundantly acting SoxC transcription factors Sox4, Sox11 and Sox12. The more SoxC alleles are deleted in mouse embryos, the more severe and widespread organ hypoplasia is. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

8 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Development of the neural tube is a highly orchestrated process relying on precise, spatio-temporal expression of numerous genes as well as hierarchies of signal transduction and gene regulatory networks. Disruption of expression of a number of genes participating in these networks is believed to underlie developmental anomalies such as neural tube defects (NTDs) resulting from anomalous neural tube morphogenesis. more...

Organism:

Mus musculus; Rattus norvegicus; Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL10178

9 Samples

Download data: TXT

(Submitter supplied) We characterized the expression patterns of sense-antisense transcripts, based on available cDNA sequences, in colon (colorectal) cancer tissues and in normal tissues surrounding the cancer tissues. Although expression balances (ratios) of most of sense and antisense transcript pairs did not change between patients or between normal and cancer tissues, we found 68 sense-antisense transcripts whose expression balances were altered specifically in colon cancer tissues.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL8070

24 Samples

Download data: CSV

(Submitter supplied) Background: Recent studies have identified thousands of sense-antisense gene pairs across different genomes by computational mapping of cDNA sequences. These studies have shown that approximately 25% of all transcriptional units in the human and mouse genomes are involved in cis-sense-antisense pairs. However, the number of known sense-antisense pairs remains limited because currently available cDNA sequences represent only a fraction of the total number of transcripts comprising the transcriptome of each cell type. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL8068

24 Samples

Download data: CSV

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: BAM, TXT, XLS

(Submitter supplied) We conducted the genome-wide mRNA expression profiling in parallel with miRNA expression profiling using RNA samples extracted from rat incisor enamel organs, so as to refine the number of predicted gene targets for miRNA regulators.

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL6101

8 Samples

Download data: TXT