Effect of myeloid-specific knockout of Glul on gene expression after either DSS or H2O challenge
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 × WT vs 3 × KO vs 3 × DS vs 3 × KO_DSGroups 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 GSE253854_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 PRJNA1067574 and SRA study SRP485213. 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.
- GSM8028759 WT1 WT
- GSM8028760 WT2 WT
- GSM8028761 WT3 WT
- GSM8028762 KO1 KO
- GSM8028763 KO2 KO
- GSM8028764 KO3 KO
- GSM8028765 DS1 DS
- GSM8028766 DS2 DS
- GSM8028767 DS4 DS
- GSM8028768 KO_DS_1 KO_DS
- GSM8028769 KO_DS_2 KO_DS
- GSM8028770 KO_DS_3 KO_DS
- GSE233491 Bulk TCR-sequencing of various tissues in mice treated with 2% DSS or H2O control. 45 samples shares dss, h2o
- GSE275941 Effect of Ilf3 knockout on gene expression in AOM/DSS induced CRC 6 samples shares dss, knockout
- GSE252099 The effect of myeloid STING knockout after tumor formation on gene expression in AOM/DSS-induced CAC mice 6 samples shares dss, knockout
- GSE312324 RNA-sequencing analysis of wild-type, Lao1 knockout and Lao1/Il4i1 double knockout mice under normal and DSS-treated conditions 18 samples shares dss, knockout
- GSE250391 Effect of depletion of Rictor on gene expression during 3% DSS treatment of colonic epithelial cells. 16 samples shares dss
- GSE239475 Effects of methionine, tryptophan, and niacin deficient diets on gene expression in intestinal cells in the DSS drinking IBD mouse model. 9 samples shares dss
- 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 dss
- GSE253368 Gene expression of Cancer-associated fibroblasts from AOM/DSS autchthonous murine tumors on the single cell level (Sort-Seq) 6 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.