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Sample GSM1468953 Query DataSets for GSM1468953
Status Public on Nov 09, 2014
Title C_input
Sample type SRA
 
Source name lymphoblastoid cell line
Organism Pan troglodytes
Characteristics cell line: lymphoblastoid
antibody: none
Sex: pooled sample from all individuals
Growth protocol cell line source: LCLs from chimpanzee and rhesus macaque individuals were obtained from New Iberia Research Center (University of Louisiana at Lafayette), and New England Primate Research Center (NEPRC, Harvard Medical School)
Extracted molecule genomic DNA
Extraction protocol Chromatin was extracted using protocol described in Cain et al. 2011, except that for some samples, chromatin was sheared with a Covaris S2 (settings: 40 minutes, duty cycle 20%, intensity 8, 200 cycles/burst, 500uL at a time in 12 x 24mm tubes).
Prepared Illumina sequencing libraries as described by the ENCODE Project Consortium (2011), starting with 20 uL of ChIP output or 4 ng of pooled input sample.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Control ChIP-seq for Chimpanzee Pooled Individuals
Data processing Basecalls by Illumina CASAVA 1.7.0
Mapped reads to panTro3 and rheMac2 using BWA 0.5.9, allowing up to 2 mismatches per read (-n 2), and excluding gapped alignments (-o 0)
Discarded reads that were assigned with a quality score less than 10 or were duplicates
For Chip-Seq, MACS version 1.4.1 was used to identify sharp peaks of enrichment for H3K4me1, H3K4me3, H3K27ac, and Pol II; RSEG version 0.4.4 was used to classify enrichment of broad genomic regions of enrichment for H3K27me3
For RNA-seq, reads mapped to orthologous exons are counted and summed at gene level
For Chip-Seq, a two-step procedure is used to classify the enriched regions/peaks for each mark
Genome_build: panTro3 and rheMac2 (and hg19 for H_input)
Supplementary_files_format_and_content: bed file format; for ChipSeq they contain peaks and enriched regions identified for each marker; for RNA-seq, they contain number of reads mapped to each gene
 
Submission date Aug 08, 2014
Last update date May 15, 2019
Contact name Xiang Zhou
E-mail(s) xzhousph@umich.edu
Phone 734-764-7067
Organization name UNIVERSITY OF MICHIGAN
Department Biostatistics
Street address 1415 Washington Heights
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL16809
Series (1)
GSE60269 Epigenetic modifications are associated with inter-species gene expression variation in primates
Relations
BioSample SAMN02979417
SRA SRX673278

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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