U.S. flag

An official website of the United States government

Format
Items per page
Sort by

Send to:

Choose Destination

Links from GEO DataSets

Items: 20

1.

Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes [RNA]

(Submitter supplied) We report high-throughput profiling of gene expression from whole zebrafish ventricles. We profile mRNA in uninjured ventricles and those undergoing regeneration 14 days after genetic ablation. This study provides a framework for understanding transcriptional changes during adult models of regeneration.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21741
4 Samples
Download data: TXT
Series
Accession:
GSE81865
ID:
200081865
2.

Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL21741
16 Samples
Download data: BED
Series
Accession:
GSE81893
ID:
200081893
3.

Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes [H3K27Ac]

(Submitter supplied) We report high-throughput profiling of acetylation of lysine 27 on histone H3 from whole zebrafish ventricles. The H3K27Ac mark has been shown to be present at active enhancer elements and including regions of active chromatin. We profile H3K27Ac in uninjured cardiomyocytes and those undergoing regeneration 14 days after genetic ablation. This study provides a framework for understanding chromatin transitions during adult models of regeneration.
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21741
2 Samples
Download data: BED
Series
Accession:
GSE81863
ID:
200081863
4.

Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes [H33]

(Submitter supplied) We report high-throughput profiling of transgenic histone H3.3 in zebrafish cardiomyocytes. The replacement histone H3.3 is deposited at sites of nucleosome turnover including regions of active chromatin. We profile H3.3 in uninjured cardiomyocytes, those undergoing regeneration 14 days after genetic ablation and those proliferating 7 days after Nrg1 stimulated hyperplasia. This study provides a framework for understanding chromatin transitions during adult models of regeneration.
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL21741
10 Samples
Download data: BED
Series
Accession:
GSE81862
ID:
200081862
5.

Transcription profiling of zebrafish fin regeneration

(Submitter supplied) We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL9319
4 Samples
Download data: TXT
Series
Accession:
GSE76564
ID:
200076564
6.

Modulation of tissue repair by regeneration enhancer elements.

(Submitter supplied) We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL14875 GPL9319
8 Samples
Download data: TXT, WIG
Series
Accession:
GSE75894
ID:
200075894
7.

H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration

(Submitter supplied) Deciphering the genetic and epigenetic regulation of cardiomyocyte proliferation in organisms capable of robust cardiac renewal represents an attractive inroad towards regenerating the human heart. In the highly regenerative zebrafish heart, cardiomyocytes near the wound edge undergo dramatic changes in gene expression concomitant with sarcomere disassembly, loss of cell-cell adhesion, and detachment from the extracellular matrix (ECM), which leaves them poised to divide and give rise to new muscle cells that colonize the wound. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20828 GPL14875
19 Samples
Download data: TDF
Series
Accession:
GSE96930
ID:
200096930
8.

H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [RNA-seq]

(Submitter supplied) We identify the global transcriptional changes that occur between homeostatic and proliferative cardiomyocytes in the zebrafish heart and uncover an essential role for H3K27me3 deposition in facilitating successful myocardial regeneration. Specifically, we learned that cardiomyocyte proliferation is accompanied by downregulation of sarcomeric and cytoskeletal components and upregulation of the polycomb methylase Ezh2. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
6 Samples
Download data: CSV, TDF
Series
Accession:
GSE96929
ID:
200096929
9.

H3K27me3 deposition over sarcomeric and cytoskeletal promoters is required for cardiomyocyte cytokinesis and wound invasion during zebrafish heart regeneration [ChIP-seq]

(Submitter supplied) Deciphering the genetic and epigenetic regulation of injury-induced heart regeneration in organisms capable of robust cardiac renewal represents an attractive inroad towards regenerating the human heart. In the highly regenerative zebrafish heart, cardiomyocytes near the wound edge undergo dramatic gene expression changes concomitant with sarcomere disassembly, loss of cell-cell adhesion, and detachment from the extracellular matrix (ECM), which leaves them poised to divide and give rise to new muscle cells that colonize the wound. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20828
13 Samples
Download data: CSV, TDF
Series
Accession:
GSE96928
ID:
200096928
10.

Regulation of mouse chamber selective enhancers

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
synthetic construct; Mus musculus
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
Series
Accession:
GSE215065
ID:
200215065
11.

Chamber selective enhancers identified in vivo by AAV-MPRA

(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
Series
Accession:
GSE215033
ID:
200215033
12.

Dense, systematic mutagenesis to identify the features required for CSEs

(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
Series
Accession:
GSE215032
ID:
200215032
13.

Transposase-accessible chromatin with high-throughput sequencing for purified neonatal aCMs and vCMs

(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
Series
Accession:
GSE215031
ID:
200215031
14.

Next-generation sequencing facilitates quantitative analysis of atrial and ventricular cardiomyocytes transcriptomes

(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
Series
Accession:
GSE215021
ID:
200215021
15.

Generate 3D genome database for atrial and ventricles and using chamber selective chromatin loops link a subset of CSEs to target genes

(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
Series
Accession:
GSE215020
ID:
200215020
16.

BioChIP-seq analysis of atrial and ventricular cardiomyocytes

(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
Series
Accession:
GSE215019
ID:
200215019
17.

Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes

(Submitter supplied) Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in non-mammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide histone H3 lysine 27 acetylation (H3K27ac) occupancy as a primary SE delineator. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18413
18 Samples
Download data: BED, WIG
Series
Accession:
GSE75734
ID:
200075734
18.

Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration

(Submitter supplied) The epicardium is a mesothelial tissue layer that envelops the heart. Cardiac injury activates dynamic gene expression programs in epicardial tissue, which in the case of zebrafish enables subsequent regeneration through paracrine and vascularizing effects. To identify tissue regeneration enhancer elements (TREEs) that control injury-induced epicardial gene expression during heart regeneration, we profiled transcriptomes and chromatin accessibility in epicardial cells purified from regenerating zebrafish hearts. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL14875 GPL21741
18 Samples
Download data: BIGWIG, TXT
Series
Accession:
GSE89444
ID:
200089444
19.

Gene expression arrays of cardiomyocyte ribosome-associated RNAs during zebrafish heart regeneration

(Submitter supplied) A transgenic line cmlc2:TRAP was made to express EGFP-fused ribosomal protein L10a (EGFP-L10a) in zebrafish cardiomyocytes. Then ribosome-associated RNAs were immuoprecipitated from uninjured and injured adult cmlc2:TRAP fish to determine the differential expression changes during zebrafish heart regeneration.
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL17210
9 Samples
Download data: PAIR
Series
Accession:
GSE48914
ID:
200048914
20.

Marking of the genome by H3K4 methylation prior to embryonic gene activation

(Submitter supplied) Early zebrafish embryo development proceeds first from a maternally transcribed and stored mRNAs, and zygotic gene activation (ZGA) is initiated at the mid-blastula transition (MBT; 1000-cell stage), 3.3 h post-fertilization. Very little is known on how the zygotic genome is programmed for transcriptional activation at the MBT. To start addressing this issue, we have mapped by ChIP-chip genome-wide promoter histone methylation (H3K4me3, H3K9me3, H3K27me3, H3K36me3) and RNA Pol II profiles before ZGA (256-cell stage; 2.5 hpf), during ZGA (MBT; 3.5 hpf)) and after ZGA (Post-MBT; 5.3 hpf) . more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL10835
25 Samples
Download data: PAIR
Series
Accession:
GSE27314
ID:
200027314
Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

db=gds|term=|query=1|qty=4|blobid=MCID_672a887f098d4d3459272ed8|ismultiple=true|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
   Taxonomic Groups  [List]
Tree placeholder
    Top Organisms  [Tree]

Find related data

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Support Center