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Sample GSM1917774 Query DataSets for GSM1917774
Status Public on May 04, 2016
Title ATF3-Ctrl
Sample type SRA
 
Source name HCT116 colon cancer cells, ATF3-WT, ATF3 ChIP
Organism Homo sapiens
Characteristics cell line: HCT116
cell type: colon cancer cell line
genotype/variation: ATF3-WT
treatment: DMSO
chip antibody: ATF3
Treatment protocol ATF3-wildtype (ATF3-WT), -knockout (ATF3-KO), p53-knockout (p53-KO) cells were treated with DMSO (Ctrl) or 1.5 uM of camptothecin (CPT) for 4 h, and then crosslinked by 1 mM of di(N-succinimidyl) glutarate (DSG) for 45 min and 1% of formaldehyde for 10 min.
Growth protocol Cells were generated by AAV-mediated homologous recombination.
Extracted molecule genomic DNA
Extraction protocol Chromatin was sheared by sonication using Bioruptor to an average fragment size of 500 bp, immunoprecipitated using the indicated antibody, purified and sequenced using Illumina HiScanSQ following protocols recommended by the manufacturer.
Libraries were prepared according to Illumina's instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiScanSQ
 
Description Chromatin IP against ATF3.
Data processing Reads were aligned to the hg19 reference human genome using bwa v0.6.1.
Peak-calling by HOMER v4.1.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bedGraph files, HOMER peak output files.
 
Submission date Oct 26, 2015
Last update date May 15, 2019
Contact name Jindan Yu
E-mail(s) jindan-yu@northwestern.edu
Organization name Northwestern University
Department Division of Hematology/Oncology
Lab Jindan Yu's lab
Street address 303 E. Superior St., Lurie 5-117
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
 
Platform ID GPL15456
Series (2)
GSE74355 The Common Stress Responsive Transcription Factor ATF3 Binds Active Enhancers and Bookmarks Genomic Sites for Transcriptional Regulation [ChIP-seq]
GSE74363 The Common Stress Responsive Transcription Factor ATF3 Binds Active Enhancers and Bookmarks Genomic Sites for Transcriptional Regulation
Relations
BioSample SAMN04216079
SRA SRX1384029

Supplementary file Size Download File type/resource
GSM1917774_1152.bedGraph.gz 53.2 Mb (ftp)(http) BEDGRAPH
GSM1917774_1152_peak.txt.gz 625.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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