HIV-1 Infection Regulates Gene Expression by Altering Alternative Polyadenylation Through CPSF6 and CPSF5 Delocalization
RNA-seq (gene expression) · human · 28 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 28 samples: 7 conditions, mostly in duplicateGroups 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
- HIV-1 infection regulates gene expression by altering alternative polyadenylation correlated with CPSF6 and CPSF5 redistributionmBio · 2026
Read the full summary ↓
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 GSE313109_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1378548 and SRA study SRP653939. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 7 replicated groups read from 28 sample titles; they account for 14 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.
- GSM9361157 A549 cells, mock infected, replicate 1 A549 cells, mock infect…
- GSM9361158 A549 cells, HIV-1 WT infection for 40 h, replicate 1
- GSM9361159 A549 cells, HIV-1 N74D infection for 48 h, replicate 1 A549 cells, HIV-1 N74D …
- GSM9361160 A549 cells, HIV-1 A77V infection for 48 h, replicate 1 A549 cells, HIV-1 A77V …
- GSM9361161 A549 CPSF6-KO clone B4 cells, mock infected, replicate 1 A549 CPSF6-KO clone B4 …
- GSM9361162 A549 CPSF6-KO clone B7 cells, mock infected, replicate 1 A549 CPSF6-KO clone B7 …
- GSM9361163 A549 CPSF6-KO clone C8 cells, mock infected, replicate 1 A549 CPSF6-KO clone C8 …
- GSM9361164 A549 CPSF6-KO clone D5 cells, mock infected, replicate 1 A549 CPSF6-KO clone D5 …
- GSM9361165 A549 cells, mock infected, replicate 2 A549 cells, mock infect…
- GSM9361166 A549 cells, HIV-1 WT infection for 48 h, replicate 2
- GSM9361167 A549 cells, HIV-1 N74D infection for 48 h, replicate 2 A549 cells, HIV-1 N74D …
- GSM9361168 A549 cells, HIV-1 A77V infection for 48 h, replicate 2 A549 cells, HIV-1 A77V …
- GSM9361169 A549 CPSF6-KO clone B4 cells, mock infected, replicate 2 A549 CPSF6-KO clone B4 …
- GSM9361170 A549 CPSF6-KO clone B7 cells, mock infected, replicate 2 A549 CPSF6-KO clone B7 …
- GSM9361171 A549 CPSF6-KO clone C8 cells, mock infected, replicate 2 A549 CPSF6-KO clone C8 …
- GSM9361172 A549 CPSF6-KO clone D5 cells, mock infected, replicate 2 A549 CPSF6-KO clone D5 …
- GSM9361173 Primary T cells, mock infected, donor 1, 96 h, replicate 1
- GSM9361174 Primary T cells, HIV-1 WT infection, donor 1, 96 h, replicate 1
- GSM9361175 Primary T cells, HIV-1 N74D infection, donor 1, 96 h, replicate 1
- GSM9361176 Primary T cells, HIV-1 A77V infection, donor 1, 96 h, replicate 1
- GSM9361177 Primary T cells, mock infected, donor 2, 96 h, replicate 1
- GSM9361178 Primary T cells, HIV-1 WT infection, donor 2, 96 h, replicate 1
- GSM9361179 Primary T cells, HIV-1 N74D infection, donor 2, 96 h, replicate 1
- GSM9361180 Primary T cells, HIV-1 A77V infection, donor 2, 96 h, replicate 1
- GSM9361181 Primary T cells, mock infected, donor 3, 96 h, replicate 1
- GSM9361182 Primary T cells, HIV-1 WT infection, donor 3, 96 h, replicate 1
- GSM9361183 Primary T cells, HIV-1 N74D infection, donor 3, 96 h, replicate 1
- GSM9361184 Primary T cells, HIV-1 A77V infection, donor 3, 96 h, replicate 1
- GSE280360 The p400 complex promotes HIV-1 latency by suppressing 1 viral transcription and altering the host cell state [RNA-seq] 52 samples shares hiv-1, altering
- GSE269600 Multiplexed single-cell characterization of alternative polyadenylation regulators 52 samples shares polyadenylation, alternative
- GSE210746 Characterization of 3′UTRCES-mediated alternative polyadenylation (APA) engineering in prostate cancer and 293FT cells 15 samples shares polyadenylation, alternative
- GSE252892 TDP-43 nuclear loss in FTD-ALS causes widespread alternative polyadenylation 12 samples shares polyadenylation, alternative
- GSE334799 3' end sequencing of HeLa-NXF1-dTAG cells upon NXF1 degradation to characterize alternative polyadenylation dynamics 8 samples shares polyadenylation, alternative
- GSE252392 U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation 47 samples shares polyadenylation, alternative
- GSE252391 U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation [CUT&RUN] 24 samples shares polyadenylation, alternative
- GSE168897 Alternative polyadenylation is a minor feature of primary human muscle differentiation 24 samples shares polyadenylation, alternative
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.