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| Status |
Public on Aug 01, 2012 |
| Title |
HepG2.H3K27me3_ChIP-Seq |
| Sample type |
SRA |
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| Source name |
HepG2 cells, H3K27me3 ChIP
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: human hepatocellular liver carcinoma cells
chip antibody: anti-H3K27me3
antibody vendor: Abcam
antibody catalog #: ab6002
antibody lot #: GR39353-1
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| Growth protocol |
HepG2.2.15 cells and HepG2 cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% (v/v) foetal bovine serum (all from Gibco, USA) at 37 ℃, in an atmosphere of 5% CO2; 380µg/mL G418 was added to the HepG2.2.15 cell culture.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
In brief, 1×10^7 HepG2 and HepG2.2.15 cells were crosslinked with formaldehyde and sonicated to obtain chromatin fragments of 200 to 300 bp. Sonicated chromatin was pre-cleared and incubated with 2 µg of anti-H3K4me3 (Abcam, United Kingdom), anti-H3K27me3 (Abcam) or anti-rabbit IgG (Upstate, USA) overnight at 4℃. The crosslinks were reversed, and DNA was treated sequentially with Proteinase K and RNase A, and purified using the Qiaquick PCR-purification kit (Qiagen, Germany). ChIP samples were tested for enrichment by qPCR. For ChIP-Seq, the precipitated DNA was repaired using PNK and Klenow enzyme, and ligated to adapters according to manufacturer’s instructions. Subsequently, PCR-amplified fragments of approximately 220 bp were sequenced using Illumina HiSeq™ 2000 following the manufacturer’s protocols (www.illumina.com).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
ChIP-seq reads of ~49 bp were mapped to the University of California, Santa Cruz (UCSC) human genome (hg18) by SOAP2, which allowed a uniquely aligned read to have up to two mismatching bases. The output of the SOAP analysis data was converted to browser-extensible data (BED) files in order to view the data in the UCSC Genome Browser. The reads were binned into nonoverlapping windows of 200 bp. The number of normalized sequence reads of a gene locus=(the sequence read counts from 1 kb upstream of the transcription start site to the end of the gene / the total number of sequence reads of each modification)×the bigger total number of sequence reads of each modification between the two cells.
Genome Build:
HepG2_H3K27.bed: UCSC hg18
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| Submission date |
Jan 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ni Bing |
| E-mail(s) |
nibingxi@yahoo.com
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| Phone |
+86-23-68772348
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| Fax |
+86-23-68772348
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| Organization name |
PLA, Third Military Medical University
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| Department |
Institute of Immunology
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| Street address |
PLA, Third Military Medical University
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| City |
Chongqing |
| ZIP/Postal code |
400038 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE35462 |
Genome-wide analysis of histone methylation reveals chromatin state-based regulation of host cellular gene expression induced by hepatitis B viruses (ChIP-Seq dataset) |
| GSE35465 |
Genome-wide analysis of histone methylation reveals chromatin state-based regulation of host cellular gene expression induced by hepatitis B viruses |
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| Relations |
| SRA |
SRX118244 |
| BioSample |
SAMN00779875 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM868998_HepG2_H3K27.bed.gz |
109.7 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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