Effect of IRF3 knockdown on gene expression in an HPV16-containing epithelium
RNA-seq (gene expression) · human · 12 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
- 12 samples: 3 × RNA from NTC fibroblasts, vs 3 × RNA from IRF3 KD fibroblasts vs 3 × RNA from NTC epthelium, vs 3 × RNA from IRF3 KD epthelium,Groups 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
- Stromal Interferon Regulatory Factor 3 Can Antagonize Human Papillomavirus Replication by Supporting Epithelial-to-Mesenchymal TransitionViruses · 2025
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 GSE294286_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 PRJNA1248941 and SRA study SRP577989. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8901762 RNA from NTC fibroblasts, replicate 1 RNA from NTC fibroblast…
- GSM8901763 RNA from NTC fibroblasts, replicate 2 RNA from NTC fibroblast…
- GSM8901764 RNA from NTC fibroblasts, replicate 3 RNA from NTC fibroblast…
- GSM8901765 RNA from IRF3 KD fibroblasts replicate 1 RNA from IRF3 KD fibrob…
- GSM8901766 RNA from IRF3 KD fibroblasts replicate 2 RNA from IRF3 KD fibrob…
- GSM8901767 RNA from IRF3 KD fibroblasts replicate 3 RNA from IRF3 KD fibrob…
- GSM8901768 RNA from NTC epthelium, replicate 1 RNA from NTC epthelium,
- GSM8901769 RNA from NTC epthelium, replicate 2 RNA from NTC epthelium,
- GSM8901770 RNA from NTC epthelium, replicate 3 RNA from NTC epthelium,
- GSM8901771 RNA from IRF3 KD epthelium, replicate 1 RNA from IRF3 KD epthel…
- GSM8901772 RNA from IRF3 KD epthelium, replicate 2 RNA from IRF3 KD epthel…
- GSM8901773 RNA from IRF3 KD epthelium, replicate 3 RNA from IRF3 KD epthel…
- GSE143584 Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis 366 samples shares epithelium
- GSE282141 Effect of SLC25A1 knockdown on gene expression during differentiation of human airway basal cells 30 samples shares knockdown
- GSE285142 Effect of knocking down CERS2 or a double knockdown (KD) CERS5/6 in ventricular cardiomyocytes on gene expression under conditions of hypertrophy induced by phorbol 12-myristate 13-acetate (PMA) or controls. 24 samples shares knockdown
- GSE302095 Validation of bronchial airway gene expression associated with bronchiectasis in nasal epithelium 132 samples shares epithelium
- GSE278671 Effect of ATP7A knockdown on gene expression in glioma stem cells 12 samples shares knockdown
- GSE203625 Effect of knockdown of CENPU on gene expression of Huh-7 and MHCC-97H hepatoma cells 12 samples shares knockdown
- GSE280172 Effect of NUDT21 knockdown on gene expression in MUTZ-1 and SKM-1 myelodysplastic syndrome cells 12 samples shares knockdown
- GSE230729 Effect of FOSL1 and HDAC2 knockdown on gene expression in cancer cell lines 12 samples shares knockdown
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.