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Sample GSM1937443

Query DataSets for GSM1937443

Status

Public on Jun 01, 2016

Title

Donor7256-2A-110614

Sample type

SRA

Source name

MPP

Organism

Homo sapiens

Characteristics

cell type: multipotent progenitor cell
donorid: 7256
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)

[email protected]

Organization name

Broad Institute

Street address

415 Main Street