Effect of depletion of Rictor on gene expression during 3% DSS treatment of colonic epithelial cells.
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 16 samples: 4 × colon, WT, vs 4 × colon, cKO, vs 4 × colon, WT_DSS, vs 4 × colon, cKO_DSS,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.
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 GSE250391_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 PRJNA1053803 and SRA study SRP478499. 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.
- GSM7978545 colon, WT, rep1 colon, WT,
- GSM7978546 colon, WT, rep2 colon, WT,
- GSM7978547 colon, WT, rep3 colon, WT,
- GSM7978548 colon, WT, rep4 colon, WT,
- GSM7978549 colon, cKO, rep1 colon, cKO,
- GSM7978550 colon, cKO, rep2 colon, cKO,
- GSM7978551 colon, cKO, rep3 colon, cKO,
- GSM7978552 colon, cKO, rep4 colon, cKO,
- GSM7978553 colon, WT_DSS, rep1 colon, WT_DSS,
- GSM7978554 colon, WT_DSS, rep2 colon, WT_DSS,
- GSM7978555 colon, WT_DSS, rep3 colon, WT_DSS,
- GSM7978556 colon, WT_DSS, rep4 colon, WT_DSS,
- GSM7978557 colon, cKO_DSS, rep1 colon, cKO_DSS,
- GSM7978558 colon, cKO_DSS, rep2 colon, cKO_DSS,
- GSM7978559 colon, cKO_DSS, rep3 colon, cKO_DSS,
- GSM7978560 colon, cKO_DSS, rep4 colon, cKO_DSS,
- GSE255409 Single-cell RNA sequencing of CD45 positive cells in spleen, bone marrow, colon and periphral blood from WT and Wnt5 DKO mice under DSS treatment 10 samples shares dss, treatment
- GSE278384 Colonic Epithelial-derived FGF1 Protects against Inflammatory Bowel Disease via Driving Intestinal Stem Cells Differentiation toward Goblet Cells 12 samples shares epithelial, colonic
- GSE233491 Bulk TCR-sequencing of various tissues in mice treated with 2% DSS or H2O control. 45 samples shares dss
- GSE292614 Loss of PTDSS1 in tumor cells improves immunogenicity and response to anti-PD-1 therapy [scRNAseq] 24 samples shares dss
- GSE295477 Wumei Wan Remodels the Tumor Immune Microenvironment via the IDO1-KYN-AHR Axis in AOM/DSS-Induced Colorectal Cancer Model. 15 samples shares dss
- GSE327543 RNA-seq of GPR15L KO versus WT mice in DSS-colitis model from colon and LPMCs 12 samples shares dss
- GSE299286 Exploring the inhibitory mechanism of DSS-induced ulcerative colitis by Banxia Xiexin Decoctionthrough the combination of serumpharmacochemistry, networkpharmacology, and transcriptomics. 12 samples shares dss
- GSE264408 Single-cell RNA sequencing of healthy mouse colon and mouse colon with acute or chronic colitis induced by DSS 10 samples shares dss
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.