Transcriptomic profiling of small intestine from irinotecan-treated wild-type and Gsdme-deficient mice
RNA-seq (gene expression) · mouse · 8 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
- 8 samples: 4 × Irinotecan-treated WT mice vs 4 × Irinotecan-treated Gsdme-deficient miceGroups 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.
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 GSE342329_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 PRJNA1507375 and SRA study SRP724100. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 2 replicated groups read from 8 sample titles; they account for 8 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.
- GSM9928458 Irinotecan-treated WT mice 1 Irinotecan-treated WT m…
- GSM9928459 Irinotecan-treated WT mice 2 Irinotecan-treated WT m…
- GSM9928460 Irinotecan-treated WT mice 3 Irinotecan-treated WT m…
- GSM9928461 Irinotecan-treated WT mice 4 Irinotecan-treated WT m…
- GSM9928462 Irinotecan-treated Gsdme-deficient mice 1 Irinotecan-treated Gsdm…
- GSM9928463 Irinotecan-treated Gsdme-deficient mice 2 Irinotecan-treated Gsdm…
- GSM9928464 Irinotecan-treated Gsdme-deficient mice 3 Irinotecan-treated Gsdm…
- GSM9928465 Irinotecan-treated Gsdme-deficient mice 4 Irinotecan-treated Gsdm…
- GSE255078 RNAseq of proximal small intestine scrapings of mice fed a galactose, glucose, or lactose-containing diet during postweaning 39 samples shares intestine, small
- GSE329124 RNA-seq profiling of mouse small intestine treated with intravenous immunoglobulin (IVIg) after total abdominal irradiation 9 samples shares intestine, small
- GSE241606 Single-cell gene expression profiling of CD4+ T cells from small intestine lamina propria of mixed Bcl3-/- CD45.2+ and WT CD45.1+ bone marrow recipients [Mixed-bone-marrow_10XscRNAseq] 4 samples shares intestine, small
- GSE216972 Effect of stroke on the transcriptome in the small intestines 29 samples shares intestine, small
- GSE274960 Targeting NTRK1 Enhances Immune Checkpoint Inhibitor Efficacy in NTRK1 Wild-type Non-Small Cell Lung Cancer 19 samples shares wild-type, small
- GSE216581 Effect of stroke on the transcriptome of epithelial cells in the small intestines 12 samples shares intestine, small
- GSE247044 The crosstalk between BMP and Wnt signaling establishes the equilibrium of villus length in mammalian small intestine 12 samples shares intestine, small
- GSE216971 Effect of stroke on the transcriptome of lamina propria macrophages in the small intestines 10 samples shares intestine, small
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.