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Sample GSM1937418 Query DataSets for GSM1937418
Status Public on Jun 01, 2016
Title Donor2596-MEP-6A-150303
Sample type SRA
 
Source name MEP
Organism Homo sapiens
Characteristics cell type: megakaryocyte erythroid progenitor cell
donorid: 2596
sample type: primary human blood cell from fresh sample
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).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description library strategy: ATAC-seq
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.
 
Submission date Nov 11, 2015
Last update date May 15, 2019
Contact name Jason Daniel Buenrostro
E-mail(s) jdbuenrostro@gmail.com
Organization name Broad Institute
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL18573
Series (2)
GSE74912 ATAC-seq data
GSE75384 Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution
Relations
BioSample SAMN04262101
SRA SRX1427831

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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