NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1493023 Query DataSets for GSM1493023
Status Public on Mar 30, 2015
Title WT-MYC expressing cells FLAG ChIP (2514-WPT-10_1)
Sample type SRA
 
Source name cultured cell line
Organism Homo sapiens
Characteristics cell line: HEK293 cells, retrovirally transduced
chip antibody: M2 agarose (Sigma; F1804)
Growth protocol HEK293 cells were grown in DMEM supplemented with 10% fetal bovine serum, 100 Iu/ml penicillin, and 100 ug/ml streptomycin.
Extracted molecule genomic DNA
Extraction protocol After crosslinking and quenching of formaldehyde, lysates were prepared, sonicated to give a mean chromatin length of 200 bp, cleared by centrifugation, and cleared lysates subjected to reaction with antibodies (or IgG control) overnight.
ChIP DNA was converted into an Illumina sequencing library using the NEBNext Ultra DNA Library Prep Kit (for Illumina)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.7 with the following configurations: m(1), -3(1).
Peaks were called using SPP peak caller version 1.10.1 with the following setting: Npeak(300000), x(-500:85).
An IDR threshold of 0.5% was applied to pooled pseudoreplicates to get final sets of peaks.
Peaks that overlap with the blacklisted genomic regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include peaks called in samples.
 
Submission date Aug 28, 2014
Last update date May 15, 2019
Contact name Qingguo Wang
E-mail(s) josephw10000@gmail.com
Organization name Vanderbilt University
Department Biomedical Informatics
Street address 2525 West End AVE Suite 808
City Nashville
State/province TN
ZIP/Postal code 37221
Country USA
 
Platform ID GPL16791
Series (1)
GSE60897 Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC
Relations
BioSample SAMN03012846
SRA SRX689363

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

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