GEO DataSets

(Submitter supplied) The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. more...

Organism:

Danio rerio; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL21103

3 Samples

Download data: BW, NARROWPEAK, TXT

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

Organism:

Danio rerio; Mus musculus

Type:

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

5 related Platforms

34 Samples

Download data: BED, BW, COOL, NARROWPEAK, TXT

(Submitter supplied) The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

2 Samples

Download data: BED, COOL, TXT

(Submitter supplied) The existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, it has failed to provide clearcut evidence as to whether fishes do have bony elements related by ancestry to tetrapod hands and feet. more...

Organism:

Danio rerio; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20828 GPL19057 GPL21741

14 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. more...

Organism:

Gallus gallus; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19787 GPL19057

12 Samples

Download data: BED, BEDGRAPH, BIGWIG, NARROWPEAK

(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; Other

6 related Platforms

46 Samples

Download data: BED, BEDGRAPH, BIGWIG, BW, COOL, NARROWPEAK, TXT

(Submitter supplied) Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. more...

Organism:

Gallus gallus; Mus musculus

Type:

Other

Platforms:

GPL23499 GPL21103

2 Samples

Download data: BED, COOL, TXT

(Submitter supplied) Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. more...

Organism:

Mus musculus; Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL23499 GPL19005

15 Samples

Download data: BED, BIGWIG, NARROWPEAK

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

4 related Platforms

34 Samples

Download data: BED, BW, COOL, NARROWPEAK, TXT

(Submitter supplied) The expression of genes with a key function during development is frequently controlled by large regulatory landscapes containing multiple enhancer elements. These landscapes often match Topologically Associating Domains (TADs) and sometimes integrate range of similar enhancers, thus leading to TADs having a global regulatory specificity. To assess the relative functional importance of enhancer sequences versus the regulatory domain they are included in, we set out to transfer one particular enhancer sequence from its native domain into a TAD with a closely related, yet different functional specificity. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24973

2 Samples

Download data: BED

(Submitter supplied) The expression of genes with a key function during development is frequently controlled by large regulatory landscapes containing multiple enhancer elements. These landscapes often match Topologically Associating Domains (TADs) and sometimes integrate range of similar enhancers, thus leading to TADs having a global regulatory specificity. To assess the relative functional importance of enhancer sequences versus the regulatory domain they are included in, we set out to transfer one particular enhancer sequence from its native domain into a TAD with a closely related, yet different functional specificity. more...

Organism:

Mus musculus

Type:

Other

Platforms:

GPL21103 GPL19057

4 Samples

Download data: COOL, TXT

(Submitter supplied) The expression of genes with a key function during development is frequently controlled by large regulatory landscapes containing multiple enhancer elements. These landscapes often match Topologically Associating Domains (TADs) and sometimes integrate range of similar enhancers, thus leading to TADs having a global regulatory specificity. To assess the relative functional importance of enhancer sequences versus the regulatory domain they are included in, we set out to transfer one particular enhancer sequence from its native domain into a TAD with a closely related, yet different functional specificity. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) The expression of genes with a key function during development is frequently controlled by large regulatory landscapes containing multiple enhancer elements. These landscapes often match Topologically Associating Domains (TADs) and sometimes integrate range of similar enhancers, thus leading to TADs having a global regulatory specificity. To assess the relative functional importance of enhancer sequences versus the regulatory domain they are included in, we set out to transfer one particular enhancer sequence from its native domain into a TAD with a closely related, yet different functional specificity. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

9 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) The expression of genes with a key function during development is frequently controlled by large regulatory landscapes containing multiple enhancer elements. These landscapes often match Topologically Associating Domains (TADs) and sometimes integrate range of similar enhancers, thus leading to TADs having a global regulatory specificity. To assess the relative functional importance of enhancer sequences versus the regulatory domain they are included in, we set out to transfer one particular enhancer sequence from its native domain into a TAD with a closely related, yet different functional specificity. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL21103

13 Samples

Download data: BW, NARROWPEAK

(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; Other

Platforms:

GPL17021 GPL19057 GPL21103

86 Samples

Download data: BW, COOL, NARROWPEAK, TXT

(Submitter supplied) We used Capture Hi-C enriching the Hoxd locus and its flanking TADs to study the effects of CRISPR/Cas9-induced CTCF binding sites deletions on chromatin architecture. We analysed wildtype and homozygous mutant E9.5 trunks and E12.5 distal and proximal forelimbs.

Organism:

Mus musculus

Type:

Other

Platforms:

GPL19057 GPL21103

16 Samples

Download data: COOL, TXT

(Submitter supplied) RNA-seq analysis of the effect of CRISPR/Cas9-induced CTCF binding sites deletions on gene expression. We studied E12.5 distal or proximal forelimbs of wildtype and mutant alleles.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

36 Samples

Download data: BW, TXT

(Submitter supplied) ChIPmentation-seq analysis of CTCF and RAD21 in wildtype and mutant CTCF binding sites alleles

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

30 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) ChIP-seq analysis of CTCF wildtype in mouse embryonic posterior trunk and brain samples

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: BW, NARROWPEAK

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL19057 GPL21103

23 Samples

Download data: BW, COOL, NARROWPEAK, TAR, TXT