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Sample GSM3289770 Query DataSets for GSM3289770
Status Public on Jul 18, 2018
Title IgG control
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: IgG
myc status: activated
replicate: 1
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 IgG control
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 SAMN09671178
SRA SRX4400350

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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