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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 06, 2020 |
| Title |
ATAC-seq_Homo rep2 |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: long-term hematopoietic stem cells (LT-HSCs)
genotype: RUNX1 methylation-deficient
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
LT-HSCs were sorted and lysed in lysis buffer (10mM Tris-Cl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630).
Chromatin was extracted and processed for Tn5 transposase-mediated tagmentation and adapter incorporation for 30 min at 37 °C using the Nextera DNA Library Prep Kit (Illumina) according to the manufacturer’s protocol. Transposed DNA was amplified using NEBNext High-Fidelity 2× Master Mix (New England Biolabs). Samples were pooled and run on an Illumina HiSeq.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Reads that passed the quality filter step were mapped to the reference mouse genome sequence (mm10) using Bowtie2,11.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files were generated using bamCoverage
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| Submission date |
Apr 06, 2020 |
| Last update date |
Jul 06, 2020 |
| Contact name |
Takayoshi Matsumura |
| Organization name |
National University of Singapore
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| Department |
CSI Singapore
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| Street address |
14 Medical Drive #12-01
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| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE148201 |
Hematopoietic stem cells acquire survival advantage by loss of RUNX1 methylation identified in familial leukemia [ATAC-seq] |
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| Relations |
| BioSample |
SAMN14546397 |
| SRA |
SRX8068506 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4456040_4_homo-2.bedgraph.gz |
150.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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