|
Status |
Public on Jun 25, 2024 |
Title |
Tcell, ZNF460, activated, rep3 |
Sample type |
SRA |
|
|
Source name |
Peripheral Blood Mononuclear Cells (PBMCs)
|
Organism |
Homo sapiens |
Characteristics |
tissue: Peripheral Blood Mononuclear Cells (PBMCs) cell type: T cell treatment: anti CD3/CD38 activation
|
Treatment protocol |
Cells were stimulated with 0.1 µg/mL of anti-CD3 and anti-CD28 monoclonal antibodies in above culture medium for 1 week (activated conditions) then cultured with 10 ng/mL of human IL-7 for an additional week (resting conditions).
|
Growth protocol |
Primary T cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), antibiotics, 50 U/mL of human IL-2 and 5,000 Gy-irradiated NK and CD8 T cell depleted PBMCs, in humidified atmosphere with 5% CO2 at 37°C
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was collected, tagmented and purified using the ATAC-Seq Kit (Active Motif) PCR amplification of tagmented DNA and library preparation were performed using the ATAC-Seq Kit (Active Motif)
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|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
ATAC-Seq reads were mapped to the UCSC hg38 genome using bowtie2 vx.1.0 with the parameters --local --very-sensitive-local Duplicated reads were removed with Picard MarkDuplicates Peaks were called using macs2 vx.1.z with the parameters --nomodel –nolambda --cutoff-analysis bigWig files were generated using bamCoverage v1.x.1 with the parameter --normalizeUsing CPM Assembly: hg38 + HIV inserts Supplementary files format and content: bigwig, narrowPeak, HIV_construct_inserts_coordinates.csv
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|
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Submission date |
May 21, 2024 |
Last update date |
Jun 25, 2024 |
Contact name |
Gabriela S Silva Santos |
E-mail(s) |
gsilva@rockefeller.edu
|
Organization name |
The Rockefeller University
|
Lab |
Laboratory of Molecular Immunology
|
Street address |
1230 York Avenue
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10065 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (2) |
GSE267987 |
Transcription of HIV-1 at sites of intact latent provirus integration [ATAC-seq] |
GSE268010 |
Transcription of HIV-1 at sites of intact latent provirus integration |
|
Relations |
BioSample |
SAMN41477598 |
SRA |
SRX24623306 |