Claudin2 Upregulation: IBD and collitis-associated colon cancer [overexpression]
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: 9 conditions, mostly in duplicateGroups 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 GSE207220_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 PRJNA854176 and SRA study SRP384233. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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.
- GSM6281788 R1_ACAGTG_L001 R1_ACAGTG_L
- GSM6281789 R2_GCCAAT_L001 R2_GCCAAT_L
- GSM6281790 R3_CTTGTA_L001 R3_CTTGTA_L
- GSM6281791 R4_GTGAAA_L001 R4_GTGAAA_L
- GSM6281792 R5_CGATGT_L001 R5_CGATGT_L
- GSM6281793 R6_TGACCA_L001 R6_TGACCA_L
- GSM6281794 R7_CAGATC_L001 R7_CAGATC_L
- GSM6281795 R8_CCGTCC_L001 R8_CCGTCC_L
- GSM6281796 R9_ATCACG_L001 R9_ATCACG_L
- GSM6281797 R1_ACAGTG_L002 R1_ACAGTG_L
- GSM6281798 R2_GCCAAT_L002 R2_GCCAAT_L
- GSM6281799 R3_CTTGTA_L002 R3_CTTGTA_L
- GSM6281800 R4_GTGAAA_L002 R4_GTGAAA_L
- GSM6281801 R5_CGATGT_L002 R5_CGATGT_L
- GSM6281802 R6_TGACCA_L002 R6_TGACCA_L
- GSM6281803 R7_CAGATC_L002 R7_CAGATC_L
- GSM6281804 R8_CCGTCC_L002 R8_CCGTCC_L
- GSM6281805 R9_ATCACG_L002 R9_ATCACG_L
- GSE207221 Claudin2 Upregulation: IBD and colitis-associated colon cancer 36 samples shares claudin2, ibd, upregulation, colon
- GSE207219 Claudin2 Upregulation: IBD and colitis-associated cancer [knockout] 18 samples shares claudin2, ibd, upregulation
- 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
- GSE293093 RNA Seq of hearts upon hepatocyte-specific overexpression of REV-ERBα in cancer cachexia 29 samples shares overexpression
- GSE292013 Impact of PD-L1 overexpression on immune checkpoint inhibitor efficacy in triple-negative breast cancer using a 4T1 murine model. 12 samples shares overexpression
- GSE250195 Overexpression of miR-200s in murine ovarian cancer cells (ID8 and 28-2) 12 samples shares overexpression
- GSE273879 Cancer-induced FOXP1 disrupts and reprograms skeletal muscle circadian transcription in cachexia [skeletal muscle overexpression of FoxP1 RNA-seq] 10 samples shares overexpression
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.