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Sample GSM1621354

Query DataSets for GSM1621354

Status

Public on Apr 22, 2015

Title

GM12878_GSM1155960

Sample type

SRA

Source name

GM12878 cells

Organism

Homo sapiens

Characteristics

cell line: GM12878
treatment: none

Biomaterial provider

Coriell https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC

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, as per Buenrostro et al. (2013).

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 2000

Description

Nucleosome calling for merged dataset from GSM1155957, GSM1155958, GSM1155959, GSM1155960 ATAC-seq samples; processed data available on the series level
processed data files: GM.nucpos.bed, GM.nucsig.bw, GM.occ.bw, hg19.Scores.bw, GM.peaks.final.bed

Data processing

Library strategy: ATAC-seq

Adapters were trimmed from reads before alignment using bowtie 2 with the -X 2000 flag. Duplicate fragments for each sample were discarded, as were reads mapping to chrM, reads with mapping quality less than 30, and reads that were not properly paired.

Nucleosome calling was performed in broad open chromatin regions determined using MACS2 and filtered for high mappability. For the osmotic stress time-course, nucleosome calling was performed in regions around TSS that overlapped with broad open chromatin peaks in at least one time point.

genome build: sacCer3 for S. cerevisiae, ASM294v2.21 for S. pombe, and hg19 for human GM12878

processed data files format and content: *.nucpos.bed.gz files contain nucleosome positions. Columns are as follows: 1) chromosome 2) dyad position (0-based) 2) dyad position (1-based) 3)

processed data files format and content: *.nucleoatac_signal.bw are BigWig files containing the normalized NucleoATAC signal

processed data files format and content: *.occ.bw are BigWig files contining the nucleosome occupancy

processed data files format and content: *.peaks.final.bed are highly mappable open chromatin regions for which nucleosome calling was performed. For the osmotic stress time course, analyis was performed on regions around tss that overlapped with peaks (osmotic.tss_peak_regions.bed).

processed data files format and content: *.Scores.bw are BigWig files that contain transposase preference scores used in the sequence bias normalization for nucleosome calling. These scores represent the log of the relative probability of insertion.

Submission date

Feb 27, 2015

Last update date

May 15, 2019

Contact name

William J Greenleaf

E-mail(s)

wjg@stanford.edu

Organization name

Stanford University

Department

Genetics