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| Status |
Public on Apr 07, 2020 |
| Title |
ATAC_LSK_BMT_SKO_rep2 |
| Sample type |
SRA |
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| Source name |
bone marrow cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
cell type: LSK
genotype: SKO
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| 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.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| 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.
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| Submission date |
May 21, 2019 |
| Last update date |
Apr 08, 2020 |
| Contact name |
Yotaro Ochi |
| Organization name |
Kyoto Univiersity
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| Department |
Department of Pathology and Tumor Biology
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| Street address |
Yoshida-Konoe-cho
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| City |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
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| 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 |
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| Relations |
| BioSample |
SAMN11807818 |
| SRA |
SRX5877784 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3790085_ATAC_LSK_BMT_SKO_rep2_peaks2.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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