The gene expression profiling of 3'2'-cCAMP signaling and 2'3'-cGAMP signaling in the BMDMs of WT and STING deficienc mice
RNA-seq (gene expression) · mouse · 24 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
- Mus musculus (mouse)
- Samples
- 24 samples: 12 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
- Transcriptome-based characterization of 3'2'-cGAMP signaling mediated immune responsesComputational and structural biotechnology journal · 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 GSE240884_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 PRJNA1005640 and SRA study SRP455208. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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.
- GSM7711272 STKO_3h_23cgamp1 STKO_3h_23cgamp
- GSM7711273 STKO_3h_23cgamp2 STKO_3h_23cgamp
- GSM7711274 STKO_3h_32cgamp1 STKO_3h_32cgamp
- GSM7711275 STKO_3h_32cgamp2 STKO_3h_32cgamp
- GSM7711276 STKO_3h_Control1 STKO_3h_Control
- GSM7711277 STKO_3h_Control2 STKO_3h_Control
- GSM7711278 STKO_9h_23cgamp1 STKO_9h_23cgamp
- GSM7711279 STKO_9h_23cgamp2 STKO_9h_23cgamp
- GSM7711280 STKO_9h_32cgamp1 STKO_9h_32cgamp
- GSM7711281 STKO_9h_32cgamp2 STKO_9h_32cgamp
- GSM7711282 STKO_9h_Control1 STKO_9h_Control
- GSM7711283 STKO_9h_Control2 STKO_9h_Control
- GSM7711284 WT_3h_23cgamp1 WT_3h_23cgamp
- GSM7711285 WT_3h_23cgamp2 WT_3h_23cgamp
- GSM7711286 WT_3h_32cgamp1 WT_3h_32cgamp
- GSM7711287 WT_3h_32cgamp2 WT_3h_32cgamp
- GSM7711288 WT_3h_Control1 WT_3h_Control
- GSM7711289 WT_3h_Control2 WT_3h_Control
- GSM7711290 WT_9h_23cgamp1 WT_9h_23cgamp
- GSM7711291 WT_9h_23cgamp2 WT_9h_23cgamp
- GSM7711292 WT_9h_32cgamp1 WT_9h_32cgamp
- GSM7711293 WT_9h_32cgamp2 WT_9h_32cgamp
- GSM7711294 WT_9h_Control1 WT_9h_Control
- GSM7711295 WT_9h_Control2 WT_9h_Control
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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.