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Sample GSM1045363 Query DataSets for GSM1045363
Status Public on Jan 17, 2013
Title RUNX1
Sample type SRA
 
Source name Jurkat_RUNX1_ChIP
Organism Homo sapiens
Characteristics cell line: Jurkat Trex (Invitrogen)
chip antibody: RUNX1
chip antibody vendor: Santa Cruz
chip antibody cat. #: sc-8563
Treatment protocol cells were induced with 1 ug/mL doxycycline for ~16 hours to allow for use as an appropriate comparison control with any other Jurkat Trex lines that carry a Tet-inducible construct.
Growth protocol cells were maintained in RPMI-1640 media containing 10% FBS, penicillin, streptomycin, and 10 ug/mL Blasticidin
Extracted molecule genomic DNA
Extraction protocol Approximately 1e8 cells in 100ml of media (approx 1e6 cells/ml) were treated with 1% formaldehyde for 15 minutes. Solubilized chromatin was prepared by incubation with lysis buffers, a few cycles of sonication and MNase treatment to obtain an average DNA size of ~1kb. ChIP was performed with anti-RUNX1 polyclonals.
Purified ChIP or input DNA was further sheared to an average size of ~200bp using a BioRuptor. The ends of the DNA fragments were polished using an Epicentre End-IT kit, polyadenylated with dATP and Klenow exo- and ligated to adapters, followed by 10 rounds of PCR with high fidelty Taq.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Sample 1
Data processing reads were mapped to hg19 using bowtie version 0.12.7
peaks were called for each replicate separately using the same input control with PeakRanger 1.15
Consensus peaks of each replicate were identified using the bedtools 2.17.0 utility intersectBed with a minimum overlap of 200. The start position of the consensus region is the minimum position of the two replicates and the end position is the maximum of the two replicates.
Consensus peaks were filtered such that both replicate peaks had a PeakRanger FDR value of 1e-7 or better.
FDR-filtered consensus peak regions were used to discover the top scoring motif with CUDA-MEME 2.7.3, and these peaks were filtered such that there was one instance of the motif TGYGGYY.
Genes were assigned to consensus peaks using GREAT version 2.0.2.
Genome_build: hg19
Supplementary_files_format_and_content: one bed file for each replicate that includes their PeakRanger FDR value; one tab file representing the consensus peaks and the identity of the replicates making them up
 
Submission date Nov 28, 2012
Last update date May 15, 2019
Contact name Nevan Krogan
E-mail(s) nevan.krogan@ucsf.edu
Phone 415-476-2980
Fax 415-514-9736
Organization name University of California, San Francisco
Department Cellular & Molecular Pharmacology
Lab Krogan
Street address 1700 4th Street
City San Francisco
ZIP/Postal code 94158
Country USA
 
Platform ID GPL11154
Series (2)
GSE42575 CBFb Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression [ChIP-seq]
GSE42576 CBFb Stabilizes HIV Vif to Counteract APOBEC3 at the Expense of RUNX1 Target Gene Expression
Relations
SRA SRX206835
BioSample SAMN01820138

Supplementary file Size Download File type/resource
GSM1045363_RUNX1_consensus_peaks.tab.txt.gz 62.3 Kb (ftp)(http) TXT
GSM1045363_RUNX1_rep1_alignment.bed.gz 912.8 Mb (ftp)(http) BED
GSM1045363_RUNX1_rep2_alignment.bed.gz 613.7 Mb (ftp)(http) BED
GSM1045363_RUNX1_rep_1_peaks.bed.gz 59.2 Kb (ftp)(http) BED
GSM1045363_RUNX1_rep_2_peaks.bed.gz 58.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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