NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2857645 Query DataSets for GSM2857645
Status Public on Jun 30, 2020
Title SW480_H3K27ac
Sample type SRA
 
Source name SW480 cell line
Organism Homo sapiens
Characteristics chip antibody: H3K27ac (Abcam Cat. No. ab4729)
tumor stage: Dukes' type B, colorectal adenocarcinoma
treatment: none
Growth protocol SW480 and SW620 cell lines were obtained from China Infrastruture of Cell Line Resources and cultured as described37. Briefly, SW480 and SW620 cells were cultured in DMEM (Gibco Cat. No. C11995500BT) supplemented with 10% fetal bovine serum (Gemini Cat. No. 900-108) and 1% penicillin/streptomycin (Gibco Cat. No. 15140-122). Cells were cultured at 37°C with 5% CO2. Cells used to inject mice were stably transfected with luciferase.
Extracted molecule genomic DNA
Extraction protocol ChIP-sequencing libraries were prepared by using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB Cat. No. E7370), according to the manufacturer’s instructions.
The sequencing was performed by Hiseq1500 (Illumina).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing Fastq files from ChIP-seq experiments were mapped to the human genomes (hg19) by using STAR41 with parameters --outFilterMismatchNoverLmax 0.05.
For the ChIP-seq of histone modification, enriched loci were identified by using the findPeaks command from HOMER (http://homer.salk.edu/homer/) with the option –style histone, 4-fold enrichment over the input sample, 4-fold enrichment over local background, at FDR = 0.001, and normalization to 10 million mapped reads per experiment.
Genomic binding peaks for transcription factor FOXA2 were identified with option -style factor, 2-fold enrichment over the input sample, 2-fold enrichment over local background, at the false discovery rate of 0.001.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files and peaks were generated using HOMER.
 
Submission date Nov 15, 2017
Last update date Jun 30, 2020
Contact name Yang Eric Li
E-mail(s) liyang01133@gmail.com
Phone +1-8589222580
Organization name Tsinghua University
Department School of Life Sciences
Lab Zhi John Lu
Street address Room 2-110, Biotechnology Building, School of Life Sciences, Tsinghua University
City Beijing
State/province Beijing
ZIP/Postal code 100084
Country China
 
Platform ID GPL18460
Series (2)
GSE106921 Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer (ChIP-Seq)
GSE106923 Tissue-specific transcription reprogramming promotes liver metastasis of colorectal cancer
Relations
BioSample SAMN08027768
SRA SRX3394270

Supplementary file Size Download File type/resource
GSM2857645_SW480_H3K27ac.regions.bed.gz 329.3 Kb (ftp)(http) BED
GSM2857645_SW480_H3K27ac.ucsc.bigWig 276.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap