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Sample GSM449526 Query DataSets for GSM449526
Status Public on Dec 18, 2009
Title Jurkat_RUNX_ChIPseq
Sample type SRA
 
Source name RUNX ChIP
Organism Homo sapiens
Characteristics cell type: Jurkat, clone E6-1 T lymphocyte
antibody: RUNX monoclonal from Nancy Speck
Growth protocol Jurkat T cells were grown in RPMI media with 10% FBS
Extracted molecule genomic DNA
Extraction protocol Crosslinked nuclei were prepared from 1E7 Jurkat T cells. Chromatin was sheared by sonication and partitioned by immunoprecipitation with antibodies bound to magentic beads. Crosslinks were revered by heating and DNA was purified by a Qiagen PCR cleanup kit. ChIP and Input DNA was prepared for sequencing using Illumina’s ChIP-seq kit. Each ChIP DNA sample was pooled from three independent replicates. 36 bp reads were generated using Illumina’s Genome Analyzer II and standard pipeline software.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description Chromatin IP against RUNX
Data processing Alignment (*sorted.txt files): Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. See GSE17954 supplementary readme file for column descriptions (GSE17954_README_Sorted.txt).
Peak detection (*EmpFDR* files) was performed using the Useq application package (http://useq.sourceforge.net). File descriptions are available at http://useq.sourceforge.net/outputFileTypeDescriptions.html
 
Submission date Sep 03, 2009
Last update date May 15, 2019
Contact name Peter Hollenhorst
E-mail(s) pchollen@iupui.edu
Organization name Indiana University
Street address 1001 E Third St, Jordan Hall 104
City Bloomington
State/province IN
ZIP/Postal code 47405
Country USA
 
Platform ID GPL9115
Series (1)
GSE17954 DNA specificity determinants associate with distinct transcription factor functions
Relations
SRA SRX015826
BioSample SAMN00007539

Supplementary file Size Download File type/resource
GSM449526_ChIP_RUNX_lane1_sorted.txt.gz 154.1 Mb (ftp)(http) TXT
GSM449526_ChIP_RUNX_lane2_sorted.txt.gz 235.0 Mb (ftp)(http) TXT
GSM449526_RUNX_EmpFDR_20.00_3632.txt.gz 145.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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