GEO DataSets

(Submitter supplied) We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species; 2) high quality chromatin accessibility data for mouse limb development; 3) discovery of mass heterochronic genes between fins and limbs; 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution.

Organism:

Chiloscyllium punctatum; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18480 GPL27153

30 Samples

Download data: TXT

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

Organism:

Mus musculus; Chiloscyllium punctatum

Type:

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

Platforms:

GPL21273 GPL27153 GPL18480

43 Samples

Download data: BW

(Submitter supplied) We report time-series transcriptome of developing bamboo shark fin buds and mouse forelimb buds, and open chromatin regions of developing mouse forelimb buds. The major contributions of this study are 1) transcriptomic data with an accurate orthology map for a systematic comparison between the two species; 2) high quality chromatin accessibility data for mouse limb development; 3) discovery of mass heterochronic genes between fins and limbs; 4) hourglass-shaped conservation between fins and limbs, providing insights into a general trend of gene regulatory evolution.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

13 Samples

Download data: BW

(Submitter supplied) Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. The BMP antagonist Gremlin1 (Grem1) is an important node in the gene regulatory network that controls vertebrate limb development. In this study, we used a combination of open chromatin profiling (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) in mouse and chick to identify putative cis-regulatory modules (CRMs) that regulate Grem1 in limb buds. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: BIGBED, BIGWIG

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL19057

21 Samples

Download data: BEDGRAPH, BIGWIG, WIG

(Submitter supplied) Chromatin immunoprecipitation in combination with sequencing (ChIP-seq) was used to identify the interactions of CRMs with key regulators of Grem1 expression, namely SMAD4 (mediating response to BMP signal transduction) and GLI3 (SHH signal transduction). This analysis revealed the presence of a single significantly enriched SMAD4 ChIP-seq peak in CRM2 during initiation of forelimb bud development, when BMP4 is required to initiate/upregulate the Grem1 transcription. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: BIGWIG, WIG

(Submitter supplied) Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. In this study, we identified cis regulatory modules (CRMs) within the Fmn1/Grem1 cis-regulatory landscape that participate in controlling spatiotemporal expression of Grem1. We generated different Grem1 alleles lacking either individual CRMs, combinations or entire enhancer clusters (EC1 and EC2) using CRISPR/Cas genome editing. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

9 Samples

Download data: BEDGRAPH

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

Organism:

Gallus gallus; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19787 GPL19057

10 Samples

Download data: BIGWIG

(Submitter supplied) Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. The BMP antagonist Gremlin1 (Grem1) is an important node in the gene regulatory network that controls vertebrate limb development. In this study, we used a combination of open chromatin profiling (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) in mouse and chick to identify putative cis-regulatory modules (CRMs) that regulate Grem1 in limb buds. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: BIGBED, BIGWIG

(Submitter supplied) Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. The BMP antagonist Gremlin1 (Grem1) is an important node in the gene regulatory network that controls vertebrate limb development. In this study, we used a combination of open chromatin profiling (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) in mouse and chick to identify putative cis-regulatory modules (CRMs) that regulate Grem1 in limb buds. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: BIGWIG

(Submitter supplied) Spatiotemporal gene expression programs are orchestrated by transcriptional enhancers which interact with target-gene promoters to regulate gene expression. The BMP antagonist Gremlin1 (Grem1) is an important node in the gene regulatory network that controls vertebrate limb development. In this study, we used a combination of open chromatin profiling (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) in mouse and chick to identify putative cis-regulatory modules (CRMs) that regulate Grem1 in limb buds. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19787

2 Samples

Download data: BIGWIG

(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

Platform:

GPL13112

17 Samples

Download data: BED, TXT

(Submitter supplied) The combinatorial expression of the Hox genes along the body axes, referred to as the HOX code, is a major determinant of cell fate and plays a prevailing role in generating the animal body plan. In developing limb buds, the paralogous group 13 genes of the HoxA and HoxD clusters are essential for patterning the distal-most limb structures, the digits. Inactivation of HOXA13 and HOXD13 transcription factors (HOX13) leads to complete digit agenesis in mice, but how HOX13 regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

5 Samples

Download data: TXT

(Submitter supplied) The combinatorial expression of the Hox genes along the body axes, referred to as the HOX code, is a major determinant of cell fate and plays a prevailing role in generating the animal body plan. In developing limb buds, the paralogous group 13 genes of the HoxA and HoxD clusters are essential for patterning the distal-most limb structures, the digits. Inactivation of HOXA13 and HOXD13 transcription factors (HOX13) leads to complete digit agenesis in mice, but how HOX13 regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: BED

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

Organism:

Mus musculus; Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20983 GPL19057

8 Samples

Download data: BIGWIG

(Submitter supplied) Genome-wide comparative analyses of the open chromatin profiles between equivalent stages of mouse and pig limb bud development reveal the extensive functional divergence of their limb regulomes. These alterations affect evolutionary conserved regions located in the genomic landscapes of genes with essential functions during limb development. This analysis uncovers the widespread regulatory changes that appear to underlie the morphological diversion of the artiodactyl limb from the pentadactyl blueprint of tetrapods.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: BIGWIG

(Submitter supplied) Genome-wide comparative analyses of the open chromatin profiles between equivalent stages of mouse and pig limb bud development reveal the extensive functional divergence of their limb regulomes. These alterations affect evolutionary conserved regions located in the genomic landscapes of genes with essential functions during limb development. This analysis uncovers the widespread regulatory changes that appear to underlie the morphological diversion of the artiodactyl limb from the pentadactyl blueprint of tetrapods.

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20983

4 Samples

Download data: BIGWIG

(Submitter supplied) The dataset aims at comparing gene expression in the developing lower and upper first molars of two mouse strains: DUHi and FVB. We studied molar tooth germ an early cap stage, looking for differences in activation-inhibition mechanisms that promote tooth formation. 19202 genes are in common between FVB and reference strain C57B6 and have a MGI annotation. Out of these genes, 2234 genes (11.6%) presented a significant difference of expression between the mapping on the reference strain C57B6 and the mapping on FVB strain (DESeq2, adjusted P value < 0.05, considering the mapping effect that is with 12 replicates). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 Samples

Download data: TXT

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

Organism:

Mus musculus; Gallus gallus

Type:

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

Platforms:

GPL19057 GPL19787

30 Samples

Download data: BW

(Submitter supplied) Understanding the origin of morphological diversity across vertebrates is central to evolutionary developmental biology. cis-regulatory elements (CRE) such as enhancers and promoters interpret precise spatiotemporal cues to control and coordinate gene expression. To get insights into both conserved and species-specific variations during early limb patterning and outgrowth, we leverage genome-wide comprehensive assessment of chromatin accessibility and transcriptional changes during mouse forelimb and chicken wing bud development. more...

Organism:

Mus musculus; Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19787 GPL19057

18 Samples

Download data: BW