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Sample GSM1712811 Query DataSets for GSM1712811
Status Public on Jun 17, 2015
Title C2_H3K27me3
Sample type SRA
 
Source name induced pluripotent stem cell line
Organism Pan troglodytes
Characteristics tissue: induced pluripotent stem cell line
passage: 15+8
Sex: Male
antibody: H3K27me3 (07-449, Millipore, Billerica, MA, USA)
Treatment protocol n/a
Growth protocol Standard iPSC and precursor cell line conditions as described in text
Extracted molecule genomic DNA
Extraction protocol Cells were lysed and chromatin sheared with a Covaris S2 (settings: 4 minutes, duty cycle 10%, 5 intensity, 200 cycles per burst in 4 6x16mm tubes per individual). H3K27ac- and H3K27me3-enriched regions were isolated using 5 ug of either H3K27ac antibody (ab4729, Abcam, Cambridge, MA, USA) or H3K27me3 antibody (07-449, Millipore, Billerica, MA, USA).
ChIP and input DNA from each individual were end-repaired, A-tailed and ligated to Illumina Truseq sequencing adapters before 18 cycles of PCR amplification. 200-300 bp DNA fragments were selected for sequencing.
Single end 50 bp; Input libraries were multiplexed and sequenced on one lane of an Illumina HiSeq2500 using the rapid run mode, ChIP libraries were multiplexed and sequenced on three lanes of an Illumina HiSeq2500 using the rapid run mode.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description H3K27me3-crosslinked DNA
Data processing Mapping with BWA 0.7.9
Removal of reads that did not map uniquely to the genome, had poor mapping quality or originated from PCR duplicates.
Peak calling with MACS or RSEG
Genome_build: hg19/PanTro3
Supplementary_files_format_and_content: MACS peaks and RSEG peaks bed files, summary table
 
Submission date Jun 16, 2015
Last update date May 15, 2019
Contact name Irene Gallego Romero
E-mail(s) ireneg@uchicago.edu
Phone 773 834 1984
Organization name University of Chicago
Department Human Genetics
Lab Gilad
Street address 920 E 58th St, CLSC 317
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL19148
Series (2)
GSE61343 Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics
GSE69919 Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics [ChIP-Seq]
Relations
BioSample SAMN03776726
SRA SRX1059777

Supplementary file Size Download File type/resource
GSM1712811_C3649_H3K27me3.merged.nochrM.rmdup.filter_C3649_input.merged.nochrM.rmdup.filter-domains.bed.gz 117.2 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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