Effects of 4-HDHA on gene expression in colonic tissue of colitis mice
RNA-seq (gene expression) · mouse · 10 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
- 10 samples: 10 samples, each with a distinct title — no replicated groupsGroups 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 GSE249871_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 PRJNA1051063 and SRA study SRP477321. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 10 sample titles: 10 distinct titles with little repetition. 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.
- GSM7966210 colon1 [LC_41]
- GSM7966211 colon2 [LC_42]
- GSM7966212 colon3 [LC_43]
- GSM7966213 colon4 [LC_44]
- GSM7966214 colon5 [LC_45]
- GSM7966215 colon6 [LC_46]
- GSM7966216 colon7 [LC_47]
- GSM7966217 colon8 [LC_48]
- GSM7966218 colon9 [LC_49]
- GSM7966219 colon10 [LC_50]
- GSE303533 RNA sequencing of colonic ILC2s sorted from mice with DSS-induced colitis 6 samples shares colonic, colitis
- GSE247122 Effect of acute and chronic ATF6 activation on gene expression in the colonic epithelium, in specific pathogen-free and germ-free mice. 37 samples shares colonic
- GSE254848 Differential susceptibility to colonic ulceration in mice with genetic deletion of Ptges 47 samples shares colonic
- GSE250391 Effect of depletion of Rictor on gene expression during 3% DSS treatment of colonic epithelial cells. 16 samples shares colonic
- GSE270970 A hyperactive splice variant of STAT3 promotes colonic inflammation-associated tumorigenesis in mice 10 samples shares colonic
- GSE306798 Single-cell transcriptomic gene regulatory network analysis uncovers the alteration of colonic stem and immune cell homeostasis in Nr4a1 knockout mice 8 samples shares colonic
- GSE183687 Transcriptomic profiling of isolated hepatic macrophage subsets (Kupffer cells, Monocyte-derived Macrophages and Monocytes) in common bile duct ligated (CBDL)-mice, mice with acute colitis (DSS), and combinations (CBDL+DSS) 58 samples shares colitis
- GSE300614 Cooperativity between Ras pathway mutations in colonic tumorigenesis 27 samples shares colonic
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.