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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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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: Michael Wilson

PROVIDER: E-MTAB-6078 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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