Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-seq of gata5GFP+/- cells in WT and Gata5/6 deficient zebrafish embryos during gastrulation

ABSTRACT: Gata5/6 are essential regulators in zebrafish heart development. To understand how Gata5/6 affects the chromatin accessibility and regulates cardiac gene expression, we FACS-isolated GFP+ and GFP- cells from Tg(gata5:GFP) transgenic embryos in both control and Gata5/6 deficient embryos (injected with Gata5/6 morpholinos) and conducted ATAC-seq. We performed the experiments at 8 hours post fertilization, intending to dissect the role of Gata5/6 in the earliest step in cardiac lineage specification. We did 2-3 biological replicates for each sample. ATAC-seq libraries were made using previously published protocol (Buenrostro et al., Nat. Methods, 2013. DOI: 10.1038/nmeth.2688) and sequenced on Illumina Hiseq2500.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Danio rerio

SUBMITTER: Xuefei Yuan

PROVIDER: E-MTAB-10427 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ATAC-seq of CP-A Barrett's oesophagus cells

Project description:The open chromatin of Barrett's oesophagus cell line CP-A has been profiled by ATAC-seq.

2020-09-30 | E-MTAB-8994 | biostudies-arrayexpress

ATAC-seq of human Barrett's oesophagus tissue

Project description:Barrett's esophagus is the assumed precusor to oesophageal adenocarcinoma. We profiled the open chromatin of human Barrett's biopsies to gain insight into its molecular basis.

2019-02-04 | E-MTAB-6751 | biostudies-arrayexpress

ATAC-seq of Het1A cells with overexpression of HNF4A or GATA6

Project description:To determine the ability of HNF4A and GATA6 to drive open chromatin formation, either HNF4A or GATA6 were overexpressed in normal oesophageal Het1A cells and ATAC-seq was performed.

2019-02-04 | E-MTAB-6931 | biostudies-arrayexpress

ATAC-seq of oesophageal cell lines and tissue samples

Project description:ATAC-seq in oesophageal cell lines: OE19, HEEPIC, and human eosophageal tissue samples

2017-07-07 | E-MTAB-5169 | biostudies-arrayexpress

ATAC-seq of oesophageal adenocarcinoma cell line MFD-1

Project description:The open chromatin of new esophageal adenocarcinoma cell line MFD-1 has been profiled by ATAC-seq.

2018-04-06 | E-MTAB-6720 | biostudies-arrayexpress

Determining open chromatin profiles of a specific population of cells isolated from zebrafish embryos at 10 hours post fertilization using the ATAC-seq method

Project description:Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer (10.7554/eLife.03848). Specifically, the 2.7 kb Mouse Smarcd3-F6 sequence (chr5: 24113559 -24116342 from mm9 assembly) was sub-cloned from a gateway entry vector into the Zebrafish Enhancer Detection (ZED). Tol2-mediated transgenesis was performed and stable lines were created. The Smarcd3-F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3-F6:EGFPhsc70 embryos were dissociated at 10 hours post fertilization for fluorescent activated cell sorting (FACS). 30,000-50,000 GFP positive and negative cells were collected from FACS for ATAC-seq. ATAC-seq libraries were created with Tn5 transposase and single-end sequenced on the Illumina HiSeq 2500 platform

2018-08-21 | E-MTAB-6078 | biostudies-arrayexpress

ATAC-seq of Oesophageal Cell Lines

Project description:ATAC-seq in oesophageal cell lines, OE33 (OAC), FLO1 (OAC), HET1A (Normal)

2016-09-12 | E-MTAB-4209 | biostudies-arrayexpress

ChIP-nexus analysis of fission yeast transcription factors Cbf11, Cbf11DBM, Cbf12, Cbf12DBM, Mga2 and Fkh2

Project description:Genome-wide identification of transcription factor (TF) binding sites in the genome of the fission yeast Schizosaccharomyces pombe. The ChIP-nexus method was used. TFs included were: Cbf11-TAP and Cbf12-TAP (and their DBM mutants with impaired DNA binding), TAP-Mga2, and Fkh2-TAP (as an irrelevant control TF). IPs from an untagged WT strain were also analyzed. Cbf11-related IPs were performed from exponential cultures, while Cbf12-related IPs were performed from stationary cultures. YES complex medium was used for all cultivations.

2024-04-05 | E-MTAB-13258 | biostudies-arrayexpress

RNA-seq analysis of fission yeast wild type and cbf11∆ mutant in standard and ammonium-supplemented complex media

Project description:Transcriptome analyses of the fission yeast Schizosaccharomyces pombe cells lacking the CSL transcription factor cbf11. Wild-type cells were used as a control. Both genotypes were analyzed when grown to exponential phase in the complex YES medium, or in YES supplemented with ammonium chloride. The aim was to identify Cbf11-regulated genes, and cbf11-associated phenotypes are affected by the presence of a good nitrogen source.

2024-04-05 | E-MTAB-13302 | biostudies-arrayexpress

ATAC-seq of the B104 genome and the B73 control

Project description:Leaf and root ATAC-seq libraries for the genome B104 and its control, B73 version 5 (PRJEB32225).

2023-09-01 | E-MTAB-10696 | biostudies-arrayexpress