Dataset features

Specifications


Application: ATAC-seq analysis
Number of samples: 4
Release date: Mar 31 2017
Last update date: Nov 26 2018
Access: Public
Genes: DUX4, Dux, ZSCAN4, KDM4E
Computational protocol: Trim Galore!, Bowtie2, MACS, MEME Suite, SAMtools
Dataset link Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons [ATAC-Seq]

Experimental Protocol


We ectopically overexpressed mouse DUX (mDux) in mESCs by treating stable, clonal, cells (TRE::3xHA-mDux; MERVL::EGFP) with doxycycline for 24hrs. Cells were then subjected to FACS to separate GFP-positive and GFP-negative populations (~30,000 cells/replicate; 2 replicates per condition) for ATAC-sequencing. 125bp libraries were prepped and sequenced in paired-end format. All sequencing was done on the Illumina HiSeq 2500 platform.

Repositories


GEO

GSE85624

ENA

SRP082164

BioProject

PRJNA338975

Download


Contact


Peter Hendrickson

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