GEO DataSets

(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:

GPL21103 GPL19057 GPL24247

48 Samples

Download data: TXT

(Submitter supplied) We report the application of bioChIP-seq, bulk RNA-seq, Hi-C, H3K27ac HiChIP, and Massively parallel reporter assays (MPRAs) to characterize the p300-bound regulatory regions in murine cardiomyocytes (CMs). By obtaining ChIP-seq data of coactivator p300 from seven developmental stages of mouse CMs, we defined the dynamic p300 enhancers from embryonic CMs to adult CMs. We then validated the activity of dynamic p300 enhancers with AAV9-based MPRAs, we found dynamic p300 enhancers show dynamic activity from postnatal day 0 (P0) CMs to 4-week-old CMs. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

4 Samples

Download data: TXT

(Submitter supplied) The activity of enhancers with dynamic P300 binding or mutagenized nuclear receptor motifs was assessed by massively parallel reporter assay during CM maturation.

Organism:

Adeno-associated virus 9; Mus musculus

Type:

Other

Platforms:

GPL31917 GPL19057

88 Samples

Download data: CSV

(Submitter supplied) We report the application of bioChIP-seq, bulk RNA-seq, Hi-C, and Massively parallel reporter assays (MPRAs) to characterize the p300-bound regulatory regions in murine cardiomyocytes (CMs). By obtaining ChIP-seq data of coactivator p300 from seven developmental stages of mouse CMs, we defined the dynamic p300 enhancers from embryonic CMs to adult CMs. We then validated the activity of dynamic p300 enhancers with AAV9-based MPRAs, we found dynamic p300 enhancers show dynamic activity from postnatal day 0 (P0) CMs to 4-week-old CMs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

21 Samples

Download data: TXT

(Submitter supplied) We report the application of bioChIP-seq, bulk RNA-seq, Hi-C, and Massively parallel reporter assays (MPRAs) to characterize the p300-bound regulatory regions in murine cardiomyocytes (CMs). By obtaining ChIP-seq data of coactivator p300 from seven developmental stages of mouse CMs, we defined the dynamic p300 enhancers from embryonic CMs to adult CMs. We then validated the activity of dynamic p300 enhancers with AAV9-based MPRAs, we found dynamic p300 enhancers show dynamic activity from postnatal day 0 (P0) CMs to 4-week-old CMs. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

14 Samples

Download data: BIGWIG

(Submitter supplied) We report the application of bioChIP-seq, bulk RNA-seq, Hi-C, and Massively parallel reporter assays (MPRAs) to characterize the p300-bound regulatory regions in murine cardiomyocytes (CMs). By obtaining ChIP-seq data of coactivator p300 from seven developmental stages of mouse CMs, we defined the dynamic p300 enhancers from embryonic CMs to adult CMs. We then validated the activity of dynamic p300 enhancers with AAV9-based MPRAs, we found dynamic p300 enhancers show dynamic activity from postnatal day 0 (P0) CMs to 4-week-old CMs. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21103

9 Samples

Download data: COOL

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

Organism:

Mus musculus; synthetic construct

Type:

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

Platforms:

GPL19057 GPL26526 GPL24247

82 Samples

Download data: BW, TXT

(Submitter supplied) Measurement the activity of candidate CSEs in aCMs and vCMs.

Organism:

Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL26526 GPL24247

15 Samples

Download data: TXT

(Submitter supplied) Investigate the sequence features required for CSE activity and selectivity.

Organism:

Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL24247 GPL26526

14 Samples

Download data: TXT

(Submitter supplied) Examination of chamber selective chromatin accessibility and investigate if chromatin accessibility regulates CSEs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: BW

(Submitter supplied) To investigate the chamber selective transcriptional programs, we performed RNA-seq on purified cardiomyocytes. Totally we have 5 replicates for atrial cardiomyocytes and 5 replicates for ventricular cardiomyocytes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

10 Samples

Download data: TXT

(Submitter supplied) Measurement the contribution of 3D genome structure to chamber specific transcriptional programs and CSE activity.

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) Cardiac TF and P300 chromatin occupancy in atria and ventricles.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

33 Samples

Download data: BW

(Submitter supplied) [1] Gene expression profiling in Gata4, Mef2a knockdown in HL-1 cells. HL-1 cells infected with adenovirus expressing either control siRNA or Gata4, and Gata4 & Mef2a siRNA. [2] Genome-wide maps of cardiac transcription factors binding region in HL-1 cells. We performed bio-ChIP-seq using streptavidin beads immunoprecipitation of biotinylated 5 cardiac transcription factors (fbio) and P300 antibody ChIP-seq. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL9185 GPL6246

17 Samples

Download data: CEL, GFF, TXT

(Submitter supplied) The Mediator co-activator complex directs gene specific expression by binding distal enhancer-bound transcription factors through its Med1 subunit while bridging to RNA Polymerase-II (Pol-II) at gene promoters. In addition, Mediator scaffolds epigenetic modifying enzymes that determine local DNA accessibility. We previously found that deletion of Med1 in cardiomyocytes deregulates more than 5000 genes and promotes acute heart failure and hypothesize Med1 deficiency disrupts enhancer-promoter coupling. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

7 Samples

Download data: BW

(Submitter supplied) Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering the transcriptional programs that orchestrate organ development and homeostasis. Here we used biotinylated knockin alleles of seven key TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) that regulate heart development and homeostasis to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult heart. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL13112

45 Samples

Download data: BED, BW, TXT

(Submitter supplied) How overall principles of gene regulation (the "logic") may change during ontogeny is largely unexplored. We compared transcriptomic, epigenomic and topological profiles in embryonic (EryP) and adult (EryD) erythroblasts. Despite reduced chromatin accessibility compared to EryP, distal chromatin of EryD is enriched in H3K27ac, Gata1 and Myb occupancy. In contrast to EryP-specific genes, which exhibit promoter-centric regulation through Gata1, EryD-specific genes employ distal enhancers for long-range regulation through enhancer-promoter looping, confirmed by Gata1 HiChIP. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL19057 GPL13112

39 Samples

Download data: BED, BW, HIC, TXT

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

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL13304

15 Samples

Download data: WIG

(Submitter supplied) In this study, we further characterized the hkCP and dCP enhancers, which were identified by STARR-seq, and shown to have an intrinsic capacity to interact with a specific type of core promoter depending on the presence of a DRE motif [9]. hkCP enhancers are marked by H3K4me3, associated with TAD borders, and mediate large TSS-clustered interactions to promote robust transcription. Furthermore, they contain the architectural proteins CAP-H2, Chromator, DREF and Z4. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL13304

6 Samples

Download data: HIC, TXT

(Submitter supplied) In this study, we further characterized the hkCP and dCP enhancers, which were identified by STARR-seq, and shown to have an intrinsic capacity to interact with a specific type of core promoter depending on the presence of a DRE motif [9]. hkCP enhancers are marked by H3K4me3, associated with TAD borders, and mediate large TSS-clustered interactions to promote robust transcription. Furthermore, they contain the architectural proteins CAP-H2, Chromator, DREF and Z4. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

9 Samples

Download data: WIG