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| Status |
Public on Sep 26, 2018 |
| Title |
Donor2_naive Tregs [S05] |
| Sample type |
SRA |
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| Source name |
Naïve Tregs
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| Organism |
Homo sapiens |
| Characteristics |
subject status/id: Healthy Donor 2
tissue: peripheral blood
cell type: CD4+CD25+ cells
sorted cell type: CD4+CD25hiCD127loCD45RA+ (naïve) Tregs
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| Treatment protocol |
Cells were isolated from freshly drawn blood
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were captured for each sample and libraries were sequenced on the Illumina Hiseq 2500 instrument.
Paired-end libraries (50 cycles) were prepared according to the published ATAC-seq protocol in Shih et al., Cell 2016
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
ATAC-seq was performed according to published protocol with minor modification as described in PMC4874839. Paired-end libraries (50 cycles) were prepared according to ATAC-seq protocol with three biological replicates (i.e. cells from 3 different individuals) for each library. The sequencing was performed using Illumina 2000. To obtain the open chromatin regions, reads were aligned to hg19 using Bowtie v2.2.9 with parameters [--maxins 175 --no-discordant --no-mixed]. Properly paired and uniquely mapped alignments were extracted. The open chromatin regions were identified using Homer findPeaks tool with parameters [-region -size 500 -minDist 50 -tbp 0]. All the open chromatin peaks were merged using bedtools to obtain a set of all potential peaks. For each replicate, the differential set of open chromatin regions for each pair of samples (i.e. memory vs naïve, memory vs CD161, naïve v CD161) were extracted using homer getDifferentialPeaks with parameter ?F 2 and the set of all potential peaks. For each pair of samples, the common peaks among three replicates were extracted using bedtools multiinter. All the common differential open chromatin regions were merged using bedtools and displayed using seqMINER with three clusters. To identify motifs that are enriched in each cluster, we used homer findMotifsGenome on all known motifs.
Genome_build: hg19
Supplementary_files_format_and_content: peak files
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| Submission date |
Sep 03, 2018 |
| Last update date |
Sep 27, 2018 |
| Contact name |
Mehdi Pirooznia |
| E-mail(s) |
pirooznia@gmail.com
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| Phone |
410-340-6052
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| Organization name |
National Institutes of Health
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| Street address |
12 SOUTH DR
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE119372 |
ATAC-seq data from naïve Tregs, memory Tregs and CD161+ Tregs |
| GSE119375 |
Analysis of transcriptomes and open chromatin regions of sub-populations of human Tregs |
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| Relations |
| BioSample |
SAMN09948042 |
| SRA |
SRX4634261 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3373881_s05_peaks.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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