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| Status |
Public on Jun 01, 2016 |
| Title |
SU501-pHSC-141118 |
| Sample type |
SRA |
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| Source name |
pHSC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: acute myeloid leukemia, pre-leukemic hematopoietic stem cell
donorid: SU501
sample type: primary human leukemia cell from cryopreserved sample
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed directly from FACS-purified cells
5,000 sorted cells in FACS Buffer were pelleted by centrifugation at 500 RCF for 5 minutes at 4C in a pre-cooled fixed-angle centrifuge. 50 ul transposase mixture (25 ul of 2x TD, 2.5 ul of TDE1, 0.5 ul of 1% digitonin, 22 ul of nuclease-free water) (Cat# FC-121-1030, Illumina; Cat# G9441, Promega) was added to the cells and the pellet was disrupted by pipetting. Transposition reactions were incubated at 37C for 30 minutes in an Eppendorf ThermoMixer with agitation at 300 RPM. Transposed fragments were purified and amplified as described previously (Buenrostro et al., 2015).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
library strategy: ATAC-seq
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| Data processing |
ATAC-seq data was processed as previously described (Buenrostro et al., 2015a) with notable exceptions. In brief, reads were trimmed using a custom script and aligned using Bowtie2. To call peaks, data was aggregated by each unique cell type, peak summits were called using MACS2 and filtered using a custom blacklist, as previously described (Buenrostro et al., 2015a).
Genome_build: hg19
Supplementary_files_format_and_content: Count file is a tab-delimited text file where rows represent unique genes and columns represent unique samples.
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| Submission date |
Nov 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Daniel Buenrostro |
| E-mail(s) |
jdbuenrostro@gmail.com
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| Organization name |
Broad Institute
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE74912 |
ATAC-seq data |
| GSE75384 |
Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution |
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| Relations |
| BioSample |
SAMN04262161 |
| SRA |
SRX1427904 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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