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Sample GSM1155961

Query DataSets for GSM1155961

Status

Public on Oct 01, 2013

Title

GM12878_ATACseq_500_Rep1

Sample type

SRA

Source name

GM12878, 500 cells

Organism

Homo sapiens

Characteristics

cell line: GM12878
cell type: EBV-transformed lymphoblastoid cell line
number of cells: 500

Growth protocol

GM12878 cells were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml.

Extracted molecule

genomic DNA

Extraction protocol

GM12878 cells were harvested at a concentration of 500,000 cells/ml, CD4+ T cells were isolated from 5 ml of blood using negative selection. For both cell types, 50,000 cells were used for each transposition reaction. For the GM12878 cells, an additional experiment was performed using 500 cells. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 2000

Description

insert size: 50-500
Processed data file: none

Data processing

Library strategy: ATAC-Seq
Basecalls were performed using CASAVA.
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard.
Genome-wide read density was calculated as the number of insertions found within 150bp sliding window with 20 bp step size.
Peaks were called using the ZINBA algorithm, which was first applied to each dataset independently, using the following parameters: a 300bp window, 50bp offset, background and enriched components were modeled using the intercept, while the zero-inflated component was modeled using alignability, a posterior probability of 0.8 was used to select the set of significant regions. The peak sets from the same cell-type and number of cells were merged.
Genome_build: GRCh37
Supplementary_files_format_and_content: Peak files are in UCSC broadPeak format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand, read count within peaks, -log10(1-posterior probability), -log10(qvalue).

Submission date

Jun 07, 2013

Last update date

May 15, 2019

Contact name

William J Greenleaf

E-mail(s)

wjg@stanford.edu

Organization name

Stanford University

Department

Genetics