Integrated Sensing of Viral RNA and RNase L-Driven Intron Retention Orchestrates Anti-Poxvirus Immunity
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: 14 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.
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 GSE308598_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 PRJNA1331676 and SRA study SRP622329. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 28 samples.
How we read this: 14 replicated groups read from 28 sample titles; they account for 28 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.
- GSM9248962 Uninfected Input-1 Uninfected Input
- GSM9248963 Uninfected Input-2 Uninfected Input
- GSM9248964 24hpi VacV Input-1 24hpi VacV Input
- GSM9248965 24hpi VacV Input-2 24hpi VacV Input
- GSM9248966 24hpi VacV_dE3L Input-1 24hpi VacV_dE3L Input
- GSM9248967 24hpi VacV_dE3L Input-2 24hpi VacV_dE3L Input
- GSM9248968 6hpi VacV Input-1 6hpi VacV Input
- GSM9248969 6hpi VacV Input-2 6hpi VacV Input
- GSM9248970 6hpi VacV_dE3L Input-1 6hpi VacV_dE3L Input
- GSM9248971 6hpi VacV_dE3L Input-2 6hpi VacV_dE3L Input
- GSM9248972 Uninfected J2IP-1 Uninfected J2IP
- GSM9248973 Uninfected J2IP-2 Uninfected J2IP
- GSM9248974 24hpi VacV J2IP-1 24hpi VacV J2IP
- GSM9248975 24hpi VacV J2IP-2 24hpi VacV J2IP
- GSM9248976 24hpi VacV_dE3L J2IP-1 24hpi VacV_dE3L J2IP
- GSM9248977 24hpi VacV_dE3L J2IP-2 24hpi VacV_dE3L J2IP
- GSM9248978 Uninfected PKR Input-1 Uninfected PKR Input
- GSM9248979 Uninfected PKR Input-2 Uninfected PKR Input
- GSM9248980 24hpi VacV PKR Input-1 24hpi VacV PKR Input
- GSM9248981 24hpi VacV PKR Input-2 24hpi VacV PKR Input
- GSM9248982 24hpi VacV_dE3L PKR Input-1 24hpi VacV_dE3L PKR Inp…
- GSM9248983 24hpi VacV_dE3L PKR Input-2 24hpi VacV_dE3L PKR Inp…
- GSM9248984 Uninfected PKRIP-1 Uninfected PKRIP
- GSM9248985 Uninfected PKRIP-2 Uninfected PKRIP
- GSM9248986 24hpi VacV PKRIP-1 24hpi VacV PKRIP
- GSM9248987 24hpi VacV PKRIP-2 24hpi VacV PKRIP
- GSM9248988 24hpi VacV_dE3L PKRIP-1 24hpi VacV_dE3L PKRIP
- GSM9248989 24hpi VacV_dE3L PKRIP-2 24hpi VacV_dE3L PKRIP
- GSE303766 Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates [ChIP-seq, MeRIP-seq, RNA-seq] 36 samples shares orchestrates, sensing
- GSE90914 The U6 snRNA m6A methyltransferase METTL16 regulates SAM synthetase intron retention 12 samples shares retention, intron
- GSE299997 Integrated profiling of iPSC-derived motor neurons carrying C9orf72, FUS, TARDBP, or SOD1 mutations 156 samples shares integrated
- GSE273600 Transcriptomics of specific activation of the Integrated Stress Response compared to Arsenite and Thapsigargin treatment 120 samples shares integrated
- GSE330098 Multi-tissue microphysiological system captures integrated responses to nutritional overload and metabolic therapy 108 samples shares integrated
- GSE271961 Integrated electrophysiological and genomic profiles of single cells reveal spiking tumor cells in human glioma [Patch-Seq] 95 samples shares integrated
- GSE336577 Integrated Transcriptomic and Immune Analysis Reveals Distinct Mitochondrial and Immune Signature in COVID-19 ARDS Requiring Invasive Mechanical Ventilation 94 samples shares integrated
- GSE255606 An organ-chip model of sporadic ALS using iPSC-derived spinal cord motor neurons and an integrated blood-brain-like barrier 88 samples shares integrated
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.