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Sample GSM3289767 Query DataSets for GSM3289767
Status Public on Jul 18, 2018
Title ATF4 binding after 8 hours of MYC activation, replicate 2
Sample type SRA
Source name Human colon adenocarcinoma DLD-1 cell lines (ATCC CCL-221)
Organism Homo sapiens
Characteristics tissue: Human colon adenocarcinoma DLD-1 cell lines (ATCC CCL-221)
antibody: ATF4
myc status: activated
replicate: 2
Treatment protocol DLD-1 cells and MEFs were infected with retroviruses expressing MycER. MycER was induced with 500nM of 4-hydroxytamoxifen (4-OHT, Sigma-H7904).
Growth protocol Human colon adenocarcinoma DLD-1 cell lines were purchased from American Type Culture Collection (ATCC CCL-221) and maintained in DMEM (Invitrogen #21063-388 029) supplemented with 10% FBS (Sigma) and 1% penicillin-streptomycin (Invitrogen).
Extracted molecule genomic DNA
Extraction protocol Chromatin fragments were prepared from DLD-1: MycER cells following 8hr of MYC activation (Vehicle or 4-OHT treatment). DNA was sonicated using Covaris 200 instrument at settings of Temp 5-9, PP200, DF 10, CB 200, 720sec. 50ug DNA was used for each ChIP. The following antibodies from Santa Cruz Biotechnology were used to perform ChIP at a concentration of 5ug: ATF4 (cat# sc-200x, lot# G0115, c-20), MYC (cat# sc-764, lot#D0413, N-262), Rabbit IgG (cat# sc-2027x, lot# G2516).
Library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina #E7645S and NEBNext Multiplex Oligos for Illumina #E7335S according to manufacturer’s instructions.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description ATF4 binding after 8 hours of MYC activation, replicate 2
Data processing Chip-seq data was aligned using bowtie version 0.12.9 to human genome hg38
Peak calling was done with HOMER software with IgG samples used as a control with -style factor -fdr 0.05 parameters. Comparisons between conditions were done using -fdr 0.05 -F 1 parameters
Genome_build: hg38
Supplementary_files_format_and_content: Prosessed file contains HOMER peak calling output for every non-IgG sample versus IgG control
Submission date Jul 17, 2018
Last update date Jul 18, 2018
Contact name Priyankara J Wickramasinghe
Phone 2154956837
Organization name The Wistar Institute
Department Bioinformatics
Lab Genomics
Street address 3601 Spruce Street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platform ID GPL18573
Series (1)
GSE117240 ATF4 couples MYC-dependent translational activity to bioenergetic demands during tumor progression
BioSample SAMN09671181
SRA SRX4400347

Supplementary file Size Download File type/resource
GSM3289767_pk_ATF4.8hr.2.txt.gz 52.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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