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| Status |
Public on Jan 21, 2021 |
| Title |
Activated CD4+ T cells 2 ATAC-Seq |
| Sample type |
SRA |
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| Source name |
Peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
donor: 2
cell type: naive CD4+ T cells
activation status: Activated
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed as described by Buenrostro et al (Nature Methods, 2013, PMID: 24097267).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
FASTQ files were output using standard Illumina protocols and software.
ATAC-seq reads were aligned to the human genome assembly (hg38) using Bowtie2 v2.2.5.
For samples with two technical replicates, the BAM were merged using the samtools merge function.
Mitochondrial reads, ummapped reads and low mappability (<30) reads were filtered out using the samtools view function.
Peaks were called using MACS2 –callpeak (with parameters -- nomodel, --extsize 200, and --shift 100) after merging all the filtered reads from all the samples and both donors into a single file.
The number of read counts overlapping each peak was then obtained for all ten samples using featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text (tsv) files. Columns represent the genomic location and the number of reads for each peak. Supplementary file PeakRegions.bed.gz provides the peak regions in BED format. Supplementary file PeakCounts.txt.gz provides read counts for all samples in a single file.
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| Submission date |
Feb 05, 2019 |
| Last update date |
Jan 21, 2021 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
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| Phone |
(+61 3) 9345 2326
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| Fax |
(+61 3) 9347 0852
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| URL |
http://www.wehi.edu.au
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| Organization name |
Walter and Eliza Hall Institute of Medical Research
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| Department |
Bioinformatics
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| Lab |
Smyth
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| Street address |
1G Royal Pde
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| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE126113 |
ATAC-seq profiles of B cells and naive and activated T cells from human peripheral blood |
| GSE126117 |
RNA-seq, ATAC-seq and Hi-C profiles of B cells and naïve and activated T cells from human peripheral blood |
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| Relations |
| BioSample |
SAMN10875770 |
| SRA |
SRX5336500 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3591804_CD4T_Ac2.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
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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