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Series GSE96927 Query DataSets for GSE96927
Status Public on Apr 01, 2018
Title Chromatin accessibility profiling identifies cis-regulatory modules in an early embryonic cell lineage
Organism Strongylocentrotus purpuratus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We used DNase-seq and ATAC-seq to identify a set of putative CRMs regulating skeletogenic gene expression during sea urchin embryogenesis. These CRMs, identified by differential chromatin accessibility, are likely to be regulated by two upstream TFs, Alx1 and Ets1, that are part of the skeletogenic GRN. 9/31 od these identified CRMs were validated by reporter gene assay. Our work demonstrates the value of using differential chromatin accessibility for the high-throughput identification of CRMs in embryonic tissues.
 
Overall design DNase-seq performed on U0126-treated PMC(-) S. purpuratus embryos at 28 hpf and control whole embryos at 28 hpf. There are 2 samples and 3 replicates for each sample. ATAC-seq was performed on isolated PMCs at 24 hpf and other non-PMC cells of the embryo at 24 hpf. There were 2 samples and 2 replicates per sample.
 
Contributor(s) Shashikant T, Khor J, Ettensohn CA
Citation(s) 29558892
Submission date Mar 22, 2017
Last update date May 15, 2019
Contact name Charles A Ettensohn
E-mail(s) ettensohn@cmu.edu
Organization name Carnegie Mellon University
Street address 4400 Fifth Avenue
City Pittsburgh
State/province PA
ZIP/Postal code 15213
Country USA
 
Platforms (2)
GPL19892 Illumina HiSeq 2000 (Strongylocentrotus purpuratus)
GPL23218 Illumina NextSeq 500 (Strongylocentrotus purpuratus)
Samples (10)
GSM2546185 U0126-treated PMC(-) 28 hpf embryos, replicate 1
GSM2546186 U0126-treated PMC(-) 28 hpf embryos, replicate 2
GSM2546187 U0126-treated PMC(-) 28 hpf embryos, replicate 3
Relations
BioProject PRJNA380123
SRA SRP102309

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE96927_PMC_OtherDifferentialPeaks.bed.gz 18.6 Kb (ftp)(http) BED
GSE96927_PMC_Other_RPS.bed.gz 2.9 Mb (ftp)(http) BED
GSE96927_RAW.tar 50.2 Mb (http)(custom) TAR (of BED, TXT)
GSE96927_U0126_ControlDifferentialPeaks.bed.gz 19.2 Kb (ftp)(http) BED
GSE96927_U0126_Control_RPS.bed.gz 1.5 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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