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Sample GSM3790087 Query DataSets for GSM3790087
Status Public on Apr 07, 2020
Title ATAC_LSK_BMT_DKO_rep2
Sample type SRA
 
Source name bone marrow cells
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: bone marrow
cell type: LSK
genotype: DKO
Extracted molecule genomic DNA
Extraction protocol ATAC-seq experiments were performed using LSK or CMP cells obtained from WT-, SKO-, RKO-, or DKO-transplanted mice.
Briefly, freshly isolated 10,000 cells were pelleted and fifty microliters of transposase mixture (25 ul of 2 x TD buffer, 2.5 ul of TDE1, 0.5 ul of 1% digitonin, and 22 ul of nuclease-free water) (FC-121-1030, Illumina; G9441) was added to the cells. After transposition reactions at 37°C for 30 min, transposed DNA was purified using QIAGEN MinElute Reaction Cleanup kit. Transposed fragments were PCR-amplified, and the resulting library was sequenced on Hiseq 2500.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing Reads were aligned to the mouse mm9 reference genome using bowtie2 (v2.3.3) with -X 2000 --no-mixed --very-sensitive parameters following adapter trimming using cutadapt (v1.14).
Duplicates were removed by Picard (v2.6.0), and reads on mitochondria genome or blacklisted regions (ENCODE) were removed by bedtools (v2.27.1).
Peaks were called with MACS (v2.1.1) with –nomodel –broad parameters with a q value threshold of 1 x 10–5 for individual replicate as well as merged data of all replicates.
Genome_build: mm9
Supplementary_files_format_and_content: Peaks were called with MACS (v2.1.1) with –nomodel –broad parameters with a q value threshold of 1 x 10–5 for individual replicate as well as merged data of all replicates.
 
Submission date May 21, 2019
Last update date Apr 08, 2020
Contact name Yotaro Ochi
Organization name Kyoto Univiersity
Department Department of Pathology and Tumor Biology
Street address Yoshida-Konoe-cho
City Kyoto
ZIP/Postal code 606-8501
Country Japan
 
Platform ID GPL17021
Series (2)
GSE131573 Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [ATAC-seq]
GSE131583 Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes
Relations
BioSample SAMN11807816
SRA SRX5877786

Supplementary file Size Download File type/resource
GSM3790087_ATAC_LSK_BMT_DKO_rep2_peaks2.bed.gz 1.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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