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| Status |
Public on Jun 23, 2015 |
| Title |
Donor33_Day224_Rep1 |
| Sample type |
SRA |
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| Source name |
human CD4+ T cells, normal donor
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| Organism |
Homo sapiens |
| Characteristics |
donor identifier: 33
disease state: healthy
gender: male
cell type: CD4+ T cells
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| Treatment protocol |
For T cell activation time course, CD4+ cells from donor 1 isolated as above were stimulated with ionomycin (1 ug/mL) and PMA (20 ng/mL) and collected at 0, 1, 2, 4 hours in duplicate.
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| Growth protocol |
Donors were recruited under a Stanford University IRB-approved protocol. Informed consent was obtained. Standard blood draws in green-top tube were obtained for each time point. 1-5mL of whole blood was enriched for CD4+ cells using RosetteSep Human CD4+ T Cell Enrichment Cocktail (StemCell Technology).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
CD4+ T cells were isolated from 5 ml of blood using negative selection. Around 50,000 cells were used for each transposition reaction. 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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| Data processing |
Library strategy: ATAC-Seq
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard. 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 0.99 was used to select the set of significant regions. The peak sets from the same cell-type and number of cells were merged.
Number of Raw reads in each peak was calculated using in-house generated script, and data matrix was normalized using R.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Bed files: Peak files are in tab-separated format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand.
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| Submission date |
Aug 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
kqu@stanford.edu
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| Organization name |
Stanford University
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| Department |
Dermatology
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| Lab |
Howard Chang
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| Street address |
269 Campus Dr. CCSR 2150
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE60682 |
Individuality and variation of personal regulomes in human T cells |
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| Relations |
| BioSample |
SAMN03002826 |
| SRA |
SRX685443 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1484824_Donor33_Day224_Rep1.bed.gz |
658.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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