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| Status |
Public on Jun 25, 2024 |
| Title |
Transcription of HIV-1 at sites of intact latent provirus integration [ATAC-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The study examined proviral and neighboring gene transcription at sites of intact latent HIV-1 integration in cultured T cells obtained directly from people living with HIV, as well as engineered primary T cells and cell lines and showed that the site of integration has a dominant effect on the transcriptional activity of intact HIV-1 proviruses in the latent reservoir
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| Overall design |
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).
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| Contributor(s) |
Teixeira AR, Bittar C, Silva Santos GS, Oliveira TY, Huang AS, Linden N, Ferreira IA, Murdza T, Muecksch F, Jones RB, Caskey M, Jankovic M, Nussenzweig MC |
| Citation(s) |
39141127 |
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| Submission date |
May 21, 2024 |
| Last update date |
Oct 08, 2024 |
| Contact name |
Gabriela S Silva Santos |
| E-mail(s) |
gsilva@rockefeller.edu
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| Organization name |
The Rockefeller University
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| Lab |
Laboratory of Molecular Immunology
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| Street address |
1230 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (67)
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| GSM8283320 |
Tcell, control, resting, rep1 |
| GSM8283321 |
Tcell, control, resting, rep2 |
| GSM8283322 |
Tcell, control, resting, rep3 |
| GSM8283323 |
Tcell, control, resting, rep4 |
| GSM8283324 |
Jurkat, control, rep1 |
| GSM8283325 |
Jurkat, control, rep2 |
| GSM8283326 |
Jurkat, control, rep3 |
| GSM8283327 |
Tcell, ATP2B, activated, rep1 |
| GSM8283328 |
Tcell, ATP2B, activated, rep2 |
| GSM8283329 |
Tcell, ATP2B, activated, rep3 |
| GSM8283330 |
Tcell, ATP2B, resting, rep1 |
| GSM8283331 |
Tcell, ATP2B, resting, rep2 |
| GSM8283332 |
Tcell, ATP2B, resting, rep3 |
| GSM8283333 |
Jurkat, ATP2B, rep1 |
| GSM8283334 |
Jurkat, ATP2B, rep2 |
| GSM8283335 |
Jurkat, ATP2B, rep3 |
| GSM8283336 |
Tcell, chr13, activated, rep1 |
| GSM8283337 |
Tcell, chr13, activated, rep2 |
| GSM8283338 |
Tcell, chr13, activated, rep3 |
| GSM8283339 |
Tcell, chr13, resting, rep1 |
| GSM8283340 |
Tcell, chr13, resting, rep2 |
| GSM8283341 |
Tcell, chr13, resting, rep3 |
| GSM8283342 |
Jurkat, chr13, rep1 |
| GSM8283343 |
Jurkat, chr13, rep2 |
| GSM8283344 |
Jurkat, chr13, rep3 |
| GSM8283345 |
Tcell, KCNA3, activated, rep1 |
| GSM8283346 |
Tcell, KCNA3, activated, rep2 |
| GSM8283347 |
Tcell, KCNA3, activated, rep3 |
| GSM8283348 |
Tcell, KCNA3, resting, rep1 |
| GSM8283349 |
Tcell, KCNA3, resting, rep2 |
| GSM8283350 |
Tcell, KCNA3, resting, rep3 |
| GSM8283351 |
Jurkat, KCNA3, rep1 |
| GSM8283352 |
Jurkat, KCNA3, rep2 |
| GSM8283353 |
Jurkat, KCNA3, rep3 |
| GSM8283354 |
Tcell, KDM2A, activated, rep1 |
| GSM8283355 |
Tcell, KDM2A, activated, rep2 |
| GSM8283356 |
Tcell, KDM2A, activated, rep3 |
| GSM8283357 |
Tcell, KDM2A, resting, rep1 |
| GSM8283358 |
Tcell, KDM2A, resting, rep2 |
| GSM8283359 |
Tcell, KDM2A, resting, rep3 |
| GSM8283360 |
Jurkat, KDM2A, rep1 |
| GSM8283361 |
Jurkat, KDM2A, rep2 |
| GSM8283362 |
Jurkat, KDM2A, rep3 |
| GSM8283363 |
Tcell, ZNF140, activated, rep1 |
| GSM8283364 |
Tcell, ZNF140, activated, rep2 |
| GSM8283365 |
Tcell, ZNF140, activated, rep3 |
| GSM8283366 |
Tcell, ZNF140, resting, rep1 |
| GSM8283367 |
Tcell, ZNF140, resting, rep2 |
| GSM8283368 |
Tcell, ZNF140, resting, rep3 |
| GSM8283369 |
Jurkat, ZNF140, rep1 |
| GSM8283370 |
Jurkat, ZNF140, rep2 |
| GSM8283371 |
Jurkat, ZNF140, rep3 |
| GSM8283372 |
Tcell, ZNF460, activated, rep1 |
| GSM8283373 |
Tcell, ZNF460, activated, rep2 |
| GSM8283374 |
Tcell, ZNF460, activated, rep3 |
| GSM8283375 |
Tcell, ZNF460, resting, rep1 |
| GSM8283376 |
Tcell, ZNF460, resting, rep2 |
| GSM8283377 |
Tcell, ZNF460, resting, rep3 |
| GSM8283378 |
Jurkat, ZNF460, rep1 |
| GSM8283379 |
Jurkat, ZNF460, rep2 |
| GSM8283380 |
Jurkat, ZNF460, rep3 |
| GSM8283381 |
Jurkat, ZNF407, rep1 |
| GSM8283382 |
Jurkat, ZNF407, rep2 |
| GSM8283383 |
Jurkat, ZNF407, rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE268010 |
Transcription of HIV-1 at sites of intact latent provirus integration |
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| Relations |
| BioProject |
PRJNA1114001 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE267987_HIV_construct_inserts_coordinates.csv.gz |
212 b |
(ftp)(http) |
CSV |
| GSE267987_RAW.tar |
5.8 Gb |
(http)(custom) |
TAR (of BW, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
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