Exploring the inhibitory mechanism of DSS-induced ulcerative colitis by Banxia Xiexin Decoctionthrough the combination of serumpharmacochemistry, networkpharmacology, and transcriptomics.
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × Control vs 3 × DSS vs 3 × DSS-BXD-L vs 3 × DSS-BXD-HGroups 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 GSE299286_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 PRJNA1273849 and SRA study SRP591896. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9036688 Control-1 Control
- GSM9036689 Control-2 Control
- GSM9036690 Control-3 Control
- GSM9036691 DSS-1 DSS
- GSM9036692 DSS-2 DSS
- GSM9036693 DSS-3 DSS
- GSM9036694 DSS-BXD-L-1 DSS-BXD-L
- GSM9036695 DSS-BXD-L-2 DSS-BXD-L
- GSM9036696 DSS-BXD-L-3 DSS-BXD-L
- GSM9036697 DSS-BXD-H-1 DSS-BXD-H
- GSM9036698 DSS-BXD-H-2 DSS-BXD-H
- GSM9036699 DSS-BXD-H-3 DSS-BXD-H
- GSE293468 Transcriptome Analysis Reveals the Regulatory Role of Jianpi Huazhi Wan (JPHZW) in Alleviating DSS-Induced Ulcerative Colitis 9 samples shares dss-induced, ulcerative
- 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-induced
- GSE262546 Paneth cell SIRT1 deficiency protects against DSS-induced colitis 10 samples shares dss-induced
- GSE231506 Efferct of Vista deficiency on mucosal damage in DSS-induced colitis 10 samples shares dss-induced
- GSE280748 Chick Early Amniotic Fluid Alleviates DSS-induced Colitis in Mice via T cell Receptor Pathway 10 samples shares dss-induced
- GSE247421 Alistipes putredinis protects DSS-induced colitis through mediating immune tolerance 8 samples shares dss-induced
- GSE303533 RNA sequencing of colonic ILC2s sorted from mice with DSS-induced colitis 6 samples shares dss-induced
- GSE327232 Transcriptomic profiling of splenic CD4+ T cells in DSS-induced colitis mice treated with Akkermansia muciniphila 6 samples shares dss-induced
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.