Dataset features

Specifications


Application: ChIP-seq analysis
Number of samples: 14
Release date: Feb 23 2016
Last update date: Apr 4 2018
Access: Public
Genes: FOXJ1, RFX2, MYB, MCIDAS, RAD21
Taxon: Xenopus laevis
Computational protocol: STAR, TreeView, DESeq, BWA, IGV
Dataset link Histone modification and transcription factor ChIPseq of Xenopus laevis epithelial progenitors

Experimental Protocol


Some embryos were harvested as wild-types; in other experiments, we injected embryos with mRNAs encoding FLAG-foxj1 (with and without rfx2 morpholino) or GFP-myb (with and without an inducible form of multicilin (mcidas-HGR)). We then isolated epithelial progenitors surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested chromatin at 9 hours after induction (roughly stage 18) and performed ChIPseq using antibodies against endogenous targets (H3K4me3, H3K27ac, rad21) or protein tags (FLAG, GFP). We then sequenced these libraries, aligned the reads to the X. laevis genome (version 9.1) with bwa mem and called peaks with HOMER, using input as background.

Repositories


GEO

GSE78176

ArrayExpress

E-GEOD-78176

ENA

SRP070664

BioProject

PRJNA312836

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Contact


Ian Quigley
Ian K Quigley

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