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Sample GSM663761 Query DataSets for GSM663761
Status Public on Dec 11, 2012
Title IMR90_H1.5_ChIPseq
Sample type SRA
 
Source name IMR90 human lung fibroblasts
Organism Homo sapiens
Characteristics cell line: IMR90
passages: 7-9
antibody: HIST1H1B
antibody manufacturer: Abcam
antibody catalog #: ab24175
Growth protocol H1 hESCs were plated on Matrigel (BD Biosciences)-coated plates, and maintained in mTeSR (StemCell). Before purification, cells were trypsinized to single cells and TRA-1-60 expressing cells were isolated by using MACS cell separation columns (Miltenyi Biotec). Isolated cells were tested by flow cytometry, and samples with >99% purity were used. IMR90 human primary lung embryo fibroblasts (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO2. Growing cells with 50~70% confluence were used for further assay.
Extracted molecule genomic DNA
Extraction protocol Standard chromatin immunoprecipiation protocol
~20 ng of ChIP and Input double strand DNA were end-repaired, added ‘A’ base to the 3-prime end, and ligated to adaptors by using Illumina ChIP-seq DNA Sample Prep. Kit Box 1. DNA fragments with 150 – 300 bp were selected and purified by agarose gel extraction, and amplified by PCR using Phusion polymerase (Illumina ChIP-seq DNA Sample Prep. Kit Box 1) according to manufacturer’ instrctions. Amplified DNA were purified by gel extraction and quantified by Qubit dsDNA BR assay (Invitrogen). DNA sequencing was performed by Illumina GAIIx sequencer with read length of 75 base pairs as per manufacturer’s protocol. Raw reads data were generated by the software SCS2.6. Further data analysis is available via online supporting information.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description Chromatin IP against human HIST1H1B (H1.5)
Data processing Unique sequences (duplicated sequences were removed and mapped only once to the genome) were aligned to human genome reference HG19 by using Bowtie-0.12.7 (command: bowtie -r -t -o 6 -a -m 1 --best --strata -v 2). Each chromosome was divided into windows of 100 bp. Number of reads in each window was calculated. To normalize total reads of ChIP enriched and Input DNA, the ratio of total reads from ChIP and Input DNA was calculated to generate a normalization factor which was applied to each value of the Input sample. To effectively capture local biases in the genome, we calculated the ratio of ChIP versus Input value in each window, and Poisson distribution was used to calculate a p-value for each window [2]. Significant peaks were defined as enrichment of ChIPed DNA over input DNA within a 100-base pair (bp) window at a Poisson p-value ≤ 0.001. Windows with significant p-values but with no neighboring significant peak or with no input reads were filtered out. To visualize large enrichment blocks, moving average was performed with moving window size of 10 kb and moving steps of 100 bp.
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing genomic intervals of significant peaks
 
Submission date Jan 31, 2011
Last update date May 15, 2019
Contact name Jing-Yu Li
E-mail(s) jingyuli@mednet.ucla.edu
Organization name University of California, Los Angeles
Street address 615 Charles E. Young Dr. South BSRB 357
City Los Angeles
ZIP/Postal code 90095
Country USA
 
Platform ID GPL10999
Series (2)
GSE26967 Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation
GSE26979 Human Linker Histone H1.5
Relations
SRA SRX040574
BioSample SAMN00205419

Supplementary file Size Download File type/resource
GSM663761_IMR90_H15_aligned.txt.gz 603.0 Mb (ftp)(http) TXT
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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