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Status |
Public on Oct 01, 2013 |
Title |
GM12878_ATACseq_50k_Rep4 |
Sample type |
SRA |
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Source name |
GM12878, 50k cells
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Organism |
Homo sapiens |
Characteristics |
cell line: GM12878 cell type: EBV-transformed lymphoblastoid cell line number of cells: 50K
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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.
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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.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
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Description |
insert size: 50-500 Processed data file: GM12878_ATACseq_50k_AllReps_ZINBA_pp08.bed.gz
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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).
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Submission date |
Jun 07, 2013 |
Last update date |
May 15, 2019 |
Contact name |
William J Greenleaf |
E-mail(s) |
wjg@stanford.edu
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Organization name |
Stanford University
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Department |
Genetics
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Street address |
279 Campus Dr West, Beckman Center
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City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE47753 |
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position |
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Relations |
Reanalyzed by |
GSM1621354 |
Reanalyzed by |
GSE72089 |
BioSample |
SAMN02192808 |
SRA |
SRX298003 |
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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