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Sample GSM1214534 Query DataSets for GSM1214534
Status Public on Nov 18, 2013
Title Runx3_IL2CD8+T_CHIP_Runx3_IP1
Sample type SRA
 
Source name Splenic CD8+ T cells
Organism Mus musculus
Characteristics cell type: Splenic CD8+ T cells
passages: After culture with IL-2 cells were fixed and frozen at -80°C.
strain: ICR
chip antibody: Runx3 poly clonal home made
Growth protocol Two biological replicate ChIP-Seq experiments were conducted for detection of Runx3-bound genomic regions and H3K4me1-marked regions using in-house anti Runx3 Ab and monoclonal anti-H3K4me1 Ab, rspectively, with splenic CD8+ T cells isolated by positive selection on anti-CD8 magnetic beads (BD Biosciences) >95% purity. Isolated CD8+ T cells were TCR-activated for 2 days on anti-CD3e coated plates with soluble anti-CD28 as published (Cruz-Guilloty et al., J Exp Med 206: 51-59, 2009) and then cultured for 4 additional days in the presence of 100u/ml recombinant human IL-2 (Beit Haemek, Israel). Cultured cells were then fixed and frozen at -80°C.
Extracted molecule genomic DNA
Extraction protocol Isolated cells were fixed in 1% formaldehyde and sonicated to yield DNA fragments of ~300bp. For immunoprecipitation, 48ul of anti-Runx3 Ab, anti-H3K4me1 or NIS were added to 12 mL of diluted, fragmented chromatin. DNA was purified using QIAquick spin columns (QIAGEN).
For ChIP-seq analysis, ChIP-seq libraries were prepared using the ChIP-Seq sample preparation kit (IP-102-1001, illumina) according to the manufactures instructions. Illumina sequencing was performed using Illumina genome analyzer IIx according to the manufactures instructions by loading 15 pmoles of denatured library template onto separate lanes of a flow cell. Sequencing short reads (40-42 bp) were aligned to the mouse genome (mmp9) using the ELAND program (Illumina).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description first IP experiment of Runx3
Data processing GAPipeline1.3.2: Runx3_IL-2CD8+T_CHIP_Runx3_IP1.fastq, Runx3_IL-2CD8+ T_CHIP_Runx3_IP2.fastq, Runx3_IL-2CD8+ T_CHIP_NIS1.fastq, Runx3_IL-2CD8+T_CHIP_NIS2.fastq; GAPipeline1.4.0: Runx3_CD8+T_CHIP_H3K4me1_IP1.fastq
For data analysis 7.6, 6.2 and 12.5 million Runx3, H3K4me1 and NIS IP short read (38-40bp) sequences, respectively, were aligned uniquely to the mouse genome (mm9) using ELAND. Peaks of enriched Runx3 or H3K4me1 regions were detected using the uniquely aligned sequences (sorted file) of merged biological replicates of IP versus the NIS, using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS1.4 done by scaling to small
 
Submission date Aug 22, 2013
Last update date May 15, 2019
Contact name Joseph Lotem
E-mail(s) joseph.lotem@weizmann.ac.il
Phone 972-8-934-2342
Organization name Weizmann institute of science
Department Molecular genetics
Street address P.O.B 26
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platform ID GPL11002
Series (2)
GSE50128 Genome-wide maps of Runx3 bound regions in splenic IL-2-activated CD8+ T cells
GSE50131 The transcription program of Runx3 in natural killer cells and CD8+ T cells
Relations
Reanalyzed by GSE111902
BioSample SAMN02324612
SRA SRX338024

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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