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Sample GSM1599155 Query DataSets for GSM1599155
Status Public on Jul 21, 2015
Title GM12878_K27ac_10K_Rep1
Sample type SRA
Source name GM12878
Organism Homo sapiens
Characteristics cell type: B-lymphocyte
chip antibody: H3K27ac (Abcam, catalog# ab4729, lot# GR183919-1)
Biomaterial provider
Treatment protocol None
Growth protocol GM12878 cells were grown in RPMI 1640 medium (Gibco) supplemented with 15% Fetal Bovine Serum (FBS) (Gibco), penicillin (Invitrogen), streptomycin (Invitrogen). Cultures were seeded at a concentration of between 200,000 and 500,000 viable cells per mL. Medium was changed every 2-3 days depending on cell density.
Extracted molecule genomic DNA
Extraction protocol Cells were cross-linked for 5 min with 1% formaldehyde at room temperature prior to quencing with 125mM glycin. Cross-linked cells were sonicated using Covaris S2 sonicator for 14 min with 5% duty, Intensity 3 and Bursts 200. The sonicated lysate was centrifuged at a speed of 14000×g for 10 min under 4°C. The cleared chromatin (10000 cells per 100 µl) in the supernatant was transferred to a new low-bind Eppendorf tube for subsequent microfluidic ChIP.
The ChIPed and input DNA was constructed into libraries by using the ThruPLEX FD Kit (Rubicon Genomics, Ann Arbor, MI, USA). During the amplification step, 11cycles was needed to get enough library from input DNA without over-amplification. 12~13 cycles is needed for ChIPed DNA extracted from 10000 cells. 14~15 cycles is normally required for ChIPed DNA from 1000 or less cells.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Data processing Raw sequencing reads were mapped to the human genome (hg19) or mouse genome (mm9) using Bowtie2 (v2.2.2) with default parameter setting. Only uniquly mapped reads were used for analysis
ChIP-seq peaks were identified by two peak caller, MACS (p-value < 10-5) and SPP (z-score > 4) with default parameter setting.
To generate the wig files, the human or mouse genome was divided into 100 bp bins, and the number of uniquely mapped reads were counted in each bin. We normalized the tag counts in each bin according to the total number of uniquely mapped reads. Input reads were processed in the same way and their normalized signals were subtracted from the ChIP-seq tracks.
Normalized wig files were converted to binary bigwig files
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: bigwig files
Submission date Feb 02, 2015
Last update date May 15, 2019
Contact name Kai Tan
Organization name The University of Iowa
Department Internal Medicine
Street address 3292 CBRB, 285 Newton Road
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
Platform ID GPL16791
Series (1)
GSE65516 A microfluidic device for epigenomic profiling using 100 cells
BioSample SAMN03324215
SRA SRX863154

Supplementary file Size Download File type/resource 100.0 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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