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| Status |
Public on Jul 21, 2015 |
| Title |
GM12878_K4me3_1K_Rep2 |
| Sample type |
SRA |
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| Source name |
GM12878
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| Organism |
Homo sapiens |
| Characteristics |
cell type: B-lymphocyte
chip antibody: H3K4me3 (Millipore, catalog# 07-473, lot# 2289139)
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| Biomaterial provider |
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12878
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| Treatment protocol |
None
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| 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.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| 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
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| Submission date |
Feb 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kai Tan |
| Organization name |
The University of Iowa
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| Department |
Internal Medicine
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| Street address |
3292 CBRB, 285 Newton Road
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| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE65516 |
A microfluidic device for epigenomic profiling using 100 cells |
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| Relations |
| BioSample |
SAMN03324204 |
| SRA |
SRX863149 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1599150_GM12878_K4me3_1K_Rep2.bw |
92.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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