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Series GSE78176 Query DataSets for GSE78176
Status Public on Feb 23, 2016
Title Histone modification and transcription factor ChIPseq of Xenopus laevis epithelial progenitors
Organism Xenopus laevis
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary To determine the positions of promoters and enhancers in developing Xenopus laevis epithelial progenitors, we performed ChIPseq on the histone modifications H3K4me3 and H3K27ac. We also performed ChIPseq on the transcription factors foxj1 (in the presence or absence of rfx2), myb (in the presence or absence of multicilin), and rad21.
Overall design 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.
Contributor(s) Quigley IK, Kintner C
Citation(s) 28103240
Submission date Feb 22, 2016
Last update date May 15, 2019
Contact name Ian K Quigley
Phone 858-453-4100
Organization name Salk Institute
Department Molecular Neurobiology Lab
Lab Kintner
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL18936 Illumina HiSeq 2500 (Xenopus laevis)
Samples (14)
GSM2068802 wt_H3K4me3_ChIPseq_9h_rep_1_and_2
GSM2068803 wt_H3K27ac_ChIPseq_3h_rep_1
GSM2068804 wt_H3K27ac_ChIPseq_9h_rep_1_and_2
BioProject PRJNA312836
SRA SRP070664

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Supplementary file Size Download File type/resource
GSE78176_RAW.tar 2.7 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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