|
| Status |
Public on Jun 25, 2024 |
| Title |
Tcell, ZNF140, activated, rep1 |
| 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)
|
| |
|
| 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
|
| |
|
| 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 |
SAMN41477609 |
| SRA |
SRX24623271 |
