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Sample GSM1103379 Query DataSets for GSM1103379
Status Public on May 27, 2013
Title IgG_ChIPseq
Sample type SRA
Source name BMiFLT3 (15-3) cells
Organism Mus musculus
Characteristics cell line: BMiFLT3(15-3)
cell type: proB cells from a murine BCP-ALL
genetic modification: cells transduced with Runx1-ERt2
chip-seq antibody: rabbit anti-IgG [Abcam,catalog #37415, lot #905012]
Treatment protocol 24 hours before DNA extraction, cells were either treated with 0.2 µM Tamoxifen to ensure Runx1-ERt2 translocation into the nucleus or treated with the appropriate amount of ethanol as a control.
Growth protocol Cells were routinely grown in α-MEM with 10% FCS, glutamine and sodium pyruvate.
Extracted molecule genomic DNA
Extraction protocol ChIP experiments using anti-Runx1 or anti-IgG antibodies were performed using the EZ-ChIP Kit (Upstate/Millipore) according to the manufacturer’s protocol.
Purified DNA from chromatin immunoprecipitations (10-50 ng) was adapter-ligated using the Illumina-compatible NEXTflexTM ChIP Seq-Kit (Bioo Scientific) for DNA inserts ≥70 bps.DNA fragments between 350-550 bp were isolated using PippinPrep (Sage Science) and quantified and sized on a microfluidics-based Bioanalyzer 1200 using a High Sensitivity DNA Kit (Agilent).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Illumina Casava 1.8.2 software was used for base calling.
Sequence tags were aligned to the mm9 assembly (NCBI Build 37) with Bowtie (v. 0.12.8) reporting only top scoring unique mapping tags.
The MACS algorithm was used to identify bound regions by comparing the enrichment of the Runx1-IP sample against a control IgG-IP for background correction. MACS version 1.4.01 was run with all parameters at their default settings, except m-fold, which was set at 8,30, to identify Runx1-bound regions.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file identifies Runx1-bound regions
Submission date Mar 21, 2013
Last update date May 15, 2019
Contact name Neele Margarete Kriebitzsch
Organization name Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology
Lab Molecular Pathology
Street address Martinistraße 52
City Hamburg
ZIP/Postal code 20251
Country Germany
Platform ID GPL11002
Series (2)
GSE45377 Genome-wide mapping of Runx1-bound sites in early B-cell progenitors
GSE45425 Runx1 targets in early B-cell progenitors
SRA SRX253193
BioSample SAMN01985486

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

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