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Sample GSM1545001 Query DataSets for GSM1545001
Status Public on Dec 30, 2014
Title 24 month input DNA
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: NOT APPLICABLE
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 immunoprecipitation 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 1
Data processing Reads were mapped with Bowtie2. Uniquely mapped reads were used for peak calling by Macs2 with multiple testing correction q value cutoff 0.01.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.0.6 with 1 mismatch in seed allowed, command=bowtie2 -p12 -k 2 -N 1. Peak calling was performed on uniquely aligned reads (lacking bowtie2 flag XS:i) with Macs2 version 2.0.10.20131216, command=macs2 callpeak -f BAMPE -g mm -m 2 50 --verbose 3 --bdg --SPMR -t treatment.bam -c control.bam , where treatment is immunoprecipitate and control is input DNA.
Genome_build: mm9
Supplementary_files_format_and_content: The narrowPeak are BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. Definition of some specific columns are: 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start. The bigWig files were created from the Macs2 bedgraph files, representing signal density of fragment pileup as signal per million reads More information may be found in the Macs2 documentation.
 
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)
GSE63276 Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (ChIP-Seq)
GSE63277 Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function
Relations
BioSample SAMN03178086
SRA SRX759475

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not applicable for this record

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