GEO DataSets

Analysis of neuralized embryoid bodies (EBs) treated with a Hedgehog (Hh) agonist. EBs neuralized with retinoic acid. Hh signaling is mediated by Ci/Gli zinc finger domain-containing transcription regulators. Results used to identify gene targets of Gli.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 agent sets

Platform:

GPL1261

Series:

GSE4936

8 Samples

Download data: CEL, EXP

(Submitter supplied) In studies investigating Sonic hedgehog (Shh) mediated patterning of the ventral neural tube, a process where Shh acts as a morphogen, we have investigated the transcriptional network underlying neural tube specification. Adopting an ES-cell based Shh neuronal specification assay (embryoid body; EBs) and a FLAG-tagged Gli protein (a transcriptional effector of the Shh pathway), we identified a number of direct targets of Gli action using Chromatin Immunoprecipitation (ChIP). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4245

12 Samples

Download data: BED, TXT

(Submitter supplied) This experiment was specifically designed to measure neural targets of Shh signaling, we sought to profile the genes upregulated by Hh signaling in the ventral neural tube to obtain a valid dataset. To obtain ventral-specific markers, we generated retinoic acid-treated EBs grown in the presence or absence of HH-Ag. We did not observe induction of ventral Hh markers in RA-treated constitutive Gli1FLAG EBs and used these for the control, baseline set. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2707

Platform:

GPL1261

8 Samples

Download data: CEL, EXP

(Submitter supplied) Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We have characterized the Gli-dependent cis-regulatory network through a combination of whole genome ChIP-on-chip and transcriptional profiling of the developing mouse limb. These analyses identified approximately 5,000 high quality Gli3 binding sites, including all known Gli-dependent enhancers. more...

Organism:

Mus musculus

Type:

Expression profiling by array

9 related Platforms

43 Samples

Download data: BAR, CEL

(Submitter supplied) Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We have characterized the Gli-dependent cis-regulatory network through a combination of whole genome ChIP-on-chip and transcriptional profiling of the developing mouse limb. In this dataset, we include the expression data obtained from dissected mouse forelimbs using a variety of gain- and loss-of-function hedgehog pathway mutants, as well as limbs dissected into responsive (posterior 2/3ds) and non-responsive (anterior 1/3d) Hh tissues. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

28 Samples

Download data: CEL

(Submitter supplied) Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We have characterized the Gli-dependent cis-regulatory network through a combination of whole genome ChIP-on-chip and transcriptional profiling of the developing mouse limb. These analyses identified approximately 5,000 high quality Gli3 binding sites, including all known Gli-dependent enhancers. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

8 related Platforms

15 Samples

Download data: BAR, BED, CEL

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

Organism:

Mus musculus

Type:

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

4 related Platforms

16 Samples

Download data: BED, CEL, TSV

(Submitter supplied) The objective of this study was to identify genes regulated by Sonic Hedgehog pathway stimulation in neural progenitors.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) In the vertebrate neural tube, regional Sonic hedgehog (Shh) signaling invokes a time- and concentration-dependent induction of six different cell populations mediated through Gli transcriptional regulators. Elsewhere in the embryo, Shh/Gli responses invoke different tissue appropriate regulatory programs. To elucidate Shh/Gli regulation of neural fate sepcification, we performed Gli1 ChIP-Seq analysis. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL9185 GPL13112

10 Samples

Download data: BED, TSV

(Submitter supplied) We wanted to identify differentially expressed genes in wild-type forelimbs and forelimbs briefly exposed to Shh signaling. E10.25 forelimbs were cultured in control media and media containing cyclopmaine (inhibits the Hedgehog pathway)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9318

4 Samples

Download data: CSV, TXT

(Submitter supplied) We wanted to identify differentially expressed genes in wild-type and Shh null E10.5 mouse forelimbs

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: CSV, TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9318 GPL13112

8 Samples

Download data

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL19057 GPL9250

28 Samples

Download data: BED

(Submitter supplied) Nkx2.2, Nkx6.1, and Olig2 repressors were overexpressed, singly or in combination, in in vitro-derived mouse neural progenitors to identify thier repression targets

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

15 Samples

Download data: XLSX

(Submitter supplied) Nkx2.2, Nkx6.1, and Olig2 are transcriptional repressors regulating somatic motor neuron and interneuron subtypes in neural progenitors. The purpose of this study was to identify their target genes and to elucidate their gene regulatory mechanisms, including their relationship to Sonic Hedgehog/Gli pathway.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL19057 GPL9250

13 Samples

Download data: BED, TXT

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

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL5811 GPL6096

10 Samples

Download data: BAR, BED, CEL

(Submitter supplied) Sonic hedgehog (Shh) signals via Gli transcription factors to stimulate proliferation of granule neuron precursor cells (GNPs) in the cerebellum. Deregulation of Shh target genes often results in unrestrained GNP proliferation and eventually medulloblastoma (MB), the most common pediatric brain malignancy. Gene expression profiling was coupled with transcription factor binding location analysis to determine the Gli1-controlled transcriptional regulatory networks in GNPs and medulloblastoma cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

8 Samples

Download data: CEL

(Submitter supplied) Sonic hedgehog (Shh) signals via Gli transcription factors to stimulate proliferation of granule neuron precursor cells (GNPs) in the cerebellum. Deregulation of Shh target genes often results in unrestrained GNP proliferation and eventually medulloblastoma, the most common pediatric brain malignancy. Transcription factor binding location analysis (chIP-chip) revealed 510 and 1,060 genomic loci bound by Gli1 with high confidence in murine GNP and medulloblastoma cells, respectively. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

2 Samples

Download data: BAR, BED, CEL

(Submitter supplied) mESCs treated with retinoic acid (RA) and a Shh agonist (SAG) recapitulated ventral hindbrain development and produced a population of neural progenitors with a minor presence of other cell types.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: TXT