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Sample GSM1544973 Query DataSets for GSM1544973
Status Public on Nov 14, 2014
Title DKO H3K4me3 (at 24 month age) rep3
Sample type SRA
 
Source name Hematopoietic stem cells (HSC)
Organism Mus musculus
Characteristics cell type: Murine bone marrow derived primary HSCs
cell surface marker: SP-KSL-CD150+
strain: C57BL/6
chip antibody: Millipore 07-473
Treatment protocol N/A
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic DNA were extracted from the cells and fragmented to 200-500 bp via biorupter. Followed by immunoprecipittaion with specific antibody, ChIPed DNA were successfully made library using ThruPLEX preparation kit without extra amplification (Rubicon, Ann Arbor, MI)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description technical replicate of biological replicate 2
dko_H3K4me3.peaks.bed
Data processing Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using SOAP with 2 mismatches allowed; H3K4me3 and H3K36me3 are processed by MACS and H3K27me3 are processed by SICER for peak calling. Different replicates are accepted by the peak calling programs to generate one set of peaks for each condition.
Genome_build: mm9
Supplementary_files_format_and_content: BED format with 1-3 columns as chromosome, start, end. The 4th column for sicer.bed is read count. The 4th and 5th columns for peaks.bed are MACS peak id and pvalue.
 
Submission date Nov 13, 2014
Last update date May 15, 2019
Contact name deqiang sun
E-mail(s) dsun@tamu.edu
Phone (713) 677-7439
Organization name Texas A&M University
Street address 2121 W Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL13112
Series (2)
GSE50793 Role of de novo DNA methyltransferases in hematopoietic stem cells
GSE63273 Role of de novo DNA methyltransferases in hematopoietic stem cells (ChIP-Seq)
Relations
BioSample SAMN03178030
SRA SRX759249

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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