Claudin2 Upregulation: IBD and colitis-associated cancer [knockout]
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 18 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 GSE207219_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 PRJNA854177 and SRA study SRP384236. 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 18 sample titles: 18 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.
- GSM6281770 CI2KO-1_S4_L001
- GSM6281771 CI2KO-2_S5_L001
- GSM6281772 CI2KO-3_S6_L001
- GSM6281773 Riz-19-134_S16_L001
- GSM6281774 Riz-19-136_S17_L001
- GSM6281775 Riz-19-137_S18_L001
- GSM6281776 Riz-19-140_S13_L001
- GSM6281777 Riz-19-143_S14_L001
- GSM6281778 Riz-19-144_S15_L001
- GSM6281779 Riz-19-56_S7_L001
- GSM6281780 Riz-19-57A_S11_L001
- GSM6281781 Riz-19-58_S8_L001
- GSM6281782 Riz-19-59_S9_L001
- GSM6281783 Riz-19-61_S10_L001
- GSM6281784 Riz-19-63_S12_L001
- GSM6281785 WT1_S1_L001
- GSM6281786 WT2_S2_L001
- GSM6281787 WT3_S3_L001
- GSE207221 Claudin2 Upregulation: IBD and colitis-associated colon cancer 36 samples shares claudin2, ibd, colitis-associated, upregulation
- GSE207220 Claudin2 Upregulation: IBD and collitis-associated colon cancer [overexpression] 18 samples shares claudin2, ibd, upregulation
- GSE312733 Single-cell RNA-seq of colonic tumors from epithelial HO-1 knockout and control mice in a colitis-associated cancer model 4 samples shares colitis-associated, knockout
- GSE243692 Small molecule probe for IBD risk variant GPR65 I231L alters cytokine signaling networks through positive allosteric modulation 90 samples shares ibd
- GSE223224 Thymopentin ameliorates experimental colitis by inhibiting neutrophil extracellular traps: an alternative way to restore immune balance in IBD? 12 samples shares ibd
- 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 ibd
- GSE275920 Neurogenic Monocyte Recruitment Drives Pathogenic Enteric Nervous System Remodeling in IBD 4 samples shares ibd
- GSE230302 Protective effect of Pien Tze Huang on colitis-associated colorectal cancer 20 samples shares colitis-associated
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.