Transcriptomics

Dataset Information

36

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


ABSTRACT: 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

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Danio rerio  

SUBMITTER: Xuefei Yuan   Michael D Wilson   Ian C Scott  

PROVIDER: E-MTAB-6078 | ArrayExpress | 2018-08-21

SECONDARY ACCESSION(S): ERP104574

REPOSITORIES: ArrayExpress, ENA

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Publications

Early patterning and specification of cardiac progenitors in gastrulating mesoderm.

Devine W Patrick WP   Wythe Joshua D JD   George Matthew M   Koshiba-Takeuchi Kazuko K   Bruneau Benoit G BG  

eLife 20141008


Mammalian heart development requires precise allocation of cardiac progenitors. The existence of a multipotent progenitor for all anatomic and cellular components of the heart has been predicted but its identity and contribution to the two cardiac progenitor 'fields' has remained undefined. Here we show, using clonal genetic fate mapping, that Mesp1+ cells in gastrulating mesoderm are rapidly specified into committed cardiac precursors fated for distinct anatomic regions of the heart. We identif  ...[more]

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