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Sample GSM2629609 Query DataSets for GSM2629609
Status Public on Jun 05, 2017
Title p65 treated rep2
Sample type SRA
 
Source name HepG2
Organism Homo sapiens
Characteristics chip antibody: NF-κB (Santa Cruz, C-20, sc-372)
cell type: primary epithelial cells
tissue: liver
cell line: HepG2
Treatment protocol HepG2 cells were incubated at 37°C in 5% CO2, when grown to a density of 1‒5×10^6/mL cells were treated with 10 ng/mL of TNFα in serum-free DMEM at 37 °C for 1 h. Cells were collected by pancreatic enzymes digestion and fixed in vivo with 1% formaldehyde for 10 min at room temperature, followed with 1.25 M glycine for 5 min at room temperature to stop the cross-linking. Then, cells were centrifuged at 1,610g (10 min, 4°C), washed twice in cold PBS containing 1 mM PMSF and 1 mM protease inhibitor cocktail (PIC). Cells were swelled for 20 min on ice in 0.5 mL ChIP cell lysis buffer and centrifuged at 587g (10 min, 4°C). Nuclear pellets were lysed on ice in 0.5 mL ChIP nuclei lysis buffer. The chromatin was sheared by sonication (40×30s on/30s off; Branson, USA) and lysates cleared by centrifugation at 16,100g (15 min, 4°C). Supernatants were collected and stored in aliquots at –80°C for subsequent ChIP. DNA was purified using QIA quick PCR purification kit.
Growth protocol HepG2 cells were cultured in DMEM medium, complemented with 10% FBS, 100 units/mL penicillin and 100 µg/mL streptomycin.
Extracted molecule genomic DNA
Extraction protocol 5‒10 ng of immunoprecipitated DNA were prepared ChIP-Seq libraries.
ChIP-Seq libraries were prepared with the NEBNext Ultra DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Set 2) (New England Biolabs).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description p65_treated.bigWig
Data processing Sequencing raw data was converted to fastq format and controlled for general quality features using FastQC.
ChIP-seq reads were aligned to unique position on precompiled hg19 reference index by Bowtie with the default setting allowing up to 2 mismatches.
Peaks were identified by MACS v2.1.0 at default settings by comparing specific ChIP-seq reads above with unspecific control reads derived from sequencing matching IgG samples. Peaks were called at a Poisson p-value < 10-4 and an FDR < 5% and were used for intersection analysis to determine the overlap in pair wise comparisons.
All operations on genomic intervals like measuring and counting overlap as well as measuring distances between genomic features were performed using R's GenomicRanges package. In order to identify differentially bound regions all binding regions determined for a given factor under different conditions were collapsed and the read numbers mapping to these collapsed intervals were extracted.
In case the overlap of multiple binding factors was studied at once the multiinter function of the BedTools suite was used with the cluster option turned on.
A peak is assigned to a gene if it locates in the gene region of the gene with HOMER perl script annotatePeaks.pl.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file
 
Submission date May 16, 2017
Last update date May 15, 2019
Contact name Wei Dai
E-mail(s) [email protected]
Phone 2583793620
Organization name Southeast University
Lab State Key Laboratory of Bioelectronics
Street address Sipailou 2#,Nanjing, Jiangsu Province, P. R. China
City Nanjing
State/province Jiangsu
ZIP/Postal code 210096
Country China
 
Platform ID GPL16791
Series (2)
GSE98983 Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2 [ChIP-seq]
GSE98985 Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2
Relations
BioSample SAMN06909706
SRA SRX2830428

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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