Transcription of HIV-1 at sites of intact latent provirus integration
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 77 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 77 samples: 22 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Transcription of HIV-1 at sites of intact latent provirus integrationThe Journal of experimental medicine · 2024
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE268010_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1114035 and SRA study SRP508968. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 67 samples.
How we read this: 22 replicated groups read from 77 sample titles; they account for 67 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8283317 Tcell, control, activated, rep1 Tcell, control, activat…
- GSM8283318 Tcell, control, activated, rep2 Tcell, control, activat…
- GSM8283319 Tcell, control, activated, rep3 Tcell, control, activat…
- GSM8283320 Tcell, control, resting, rep1 Tcell, control, resting,
- GSM8283321 Tcell, control, resting, rep2 Tcell, control, resting,
- GSM8283322 Tcell, control, resting, rep3 Tcell, control, resting,
- GSM8283323 Tcell, control, resting, rep4 Tcell, control, resting,
- GSM8283324 Jurkat, control, rep1 Jurkat, control,
- GSM8283325 Jurkat, control, rep2 Jurkat, control,
- GSM8283326 Jurkat, control, rep3 Jurkat, control,
- GSM8283327 Tcell, ATP2B, activated, rep1 Tcell, ATP2B, activated,
- GSM8283328 Tcell, ATP2B, activated, rep2 Tcell, ATP2B, activated,
- GSM8283329 Tcell, ATP2B, activated, rep3 Tcell, ATP2B, activated,
- GSM8283330 Tcell, ATP2B, resting, rep1 Tcell, ATP2B, resting,
- GSM8283331 Tcell, ATP2B, resting, rep2 Tcell, ATP2B, resting,
- GSM8283332 Tcell, ATP2B, resting, rep3 Tcell, ATP2B, resting,
- GSM8283333 Jurkat, ATP2B, rep1 Jurkat, ATP2B,
- GSM8283334 Jurkat, ATP2B, rep2 Jurkat, ATP2B,
- GSM8283335 Jurkat, ATP2B, rep3 Jurkat, ATP2B,
- GSM8283336 Tcell, chr13, activated, rep1 Tcell, chr13, activated,
- GSM8283337 Tcell, chr13, activated, rep2 Tcell, chr13, activated,
- GSM8283338 Tcell, chr13, activated, rep3 Tcell, chr13, activated,
- GSM8283339 Tcell, chr13, resting, rep1 Tcell, chr13, resting,
- GSM8283340 Tcell, chr13, resting, rep2 Tcell, chr13, resting,
- GSM8283341 Tcell, chr13, resting, rep3 Tcell, chr13, resting,
- GSM8283342 Jurkat, chr13, rep1 Jurkat, chr13,
- GSM8283343 Jurkat, chr13, rep2 Jurkat, chr13,
- GSM8283344 Jurkat, chr13, rep3 Jurkat, chr13,
- GSM8283345 Tcell, KCNA3, activated, rep1 Tcell, KCNA3, activated,
- GSM8283346 Tcell, KCNA3, activated, rep2 Tcell, KCNA3, activated,
- GSM8283347 Tcell, KCNA3, activated, rep3 Tcell, KCNA3, activated,
- GSM8283348 Tcell, KCNA3, resting, rep1 Tcell, KCNA3, resting,
- GSM8283349 Tcell, KCNA3, resting, rep2 Tcell, KCNA3, resting,
- GSM8283350 Tcell, KCNA3, resting, rep3 Tcell, KCNA3, resting,
- GSM8283351 Jurkat, KCNA3, rep1 Jurkat, KCNA3,
- GSM8283352 Jurkat, KCNA3, rep2 Jurkat, KCNA3,
- GSM8283353 Jurkat, KCNA3, rep3 Jurkat, KCNA3,
- GSM8283354 Tcell, KDM2A, activated, rep1 Tcell, KDM2A, activated,
- GSM8283355 Tcell, KDM2A, activated, rep2 Tcell, KDM2A, activated,
- GSM8283356 Tcell, KDM2A, activated, rep3 Tcell, KDM2A, activated,
+ 37 more — browse all 77 samples with per-sample file links →
- GSE279688 The role of LEDGF in transcription is exploited by HIV-1 to position integration 56 samples shares hiv-1, transcription, integration
- GSE299348 Single-cell epigenetic, transcriptional, protein, and TCR states of HIV-1-infected cells in gut 117 samples shares hiv-1, transcription
- GSE239858 BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites 14 samples shares transcription, sites
- GSE328010 RNA sequencing of naïve, activated and HIV-1 infected CD4+ T cells 9 samples shares hiv-1
- GSE303478 Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome 217 samples shares transcription
- GSE296192 Hypoxic regulation of chromatin and gene transcription 98 samples shares transcription
- GSE290367 Single-cell multiomic integration identifies widespread, cell-type resolved fetal reactivation in the diseased human heart 90 samples shares integration
- GSE301298 Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency 88 samples shares transcription
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.