The DNA-damage response triggered by the caspase-activated DNAse contributes to inflammation and immune response
RNA-seq (gene expression) · human · 16 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
- 16 samples: 4 × wt 6h ut B vs 4 × wt 6h IAA B vs 4 × wt 14h ut B vs 4 × wt 14h IAA BGroups 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
- The Caspase-Activated DNase drives inflammation and contributes to defense against viral infectionCell death and differentiation · 2024
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 GSE212956_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 PRJNA878517 and SRA study SRP396291. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.
- GSM6564469 wt 6h ut BR1 wt 6h ut B
- GSM6564470 wt 6h ut BR2 wt 6h ut B
- GSM6564471 wt 6h ut BR3 wt 6h ut B
- GSM6564472 wt 6h ut BR4 wt 6h ut B
- GSM6564473 wt 6h IAA BR1 wt 6h IAA B
- GSM6564474 wt 6h IAA BR2 wt 6h IAA B
- GSM6564475 wt 6h IAA BR3 wt 6h IAA B
- GSM6564476 wt 6h IAA BR4 wt 6h IAA B
- GSM6564477 wt 14h ut BR1 wt 14h ut B
- GSM6564478 wt 14h ut BR2 wt 14h ut B
- GSM6564479 wt 14h ut BR3 wt 14h ut B
- GSM6564480 wt 14h ut BR4 wt 14h ut B
- GSM6564481 wt 14h IAA BR1 wt 14h IAA B
- GSM6564482 wt 14h IAA BR2 wt 14h IAA B
- GSM6564483 wt 14h IAA BR3 wt 14h IAA B
- GSM6564484 wt 14h IAA BR4 wt 14h IAA B
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- GSE244979 Conserved transcriptional response to adversity-related inflammation contributes to Meniere’s disease progression [RNA-Seq 2] 28 samples shares contributes
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- GSE244978 Conserved transcriptional response to adversity-related inflammation contributes to Meniere’s disease progression [RNA-Seq 1] 10 samples shares contributes
- GSE312068 Deciphering HTLV-1-associated Lung Pathology: Inflammation, Monocyte Recruitment and Differentiation Triggered by HTLV-1-exposed Alveolar Epithelial Cells 30 samples shares triggered
- GSE274713 Adipose-Tumor Crosstalk contributes to CXCL5 Mediated Immune Evasion in PDAC 30 samples shares contributes
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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.