Thymopentin ameliorates experimental colitis by inhibiting neutrophil extracellular traps: an alternative way to restore immune balance in IBD?
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 × TNB-N vs 3 × TNB-T vs 3 × DSS-N vs 3 × DSS-TGroups 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.
- Paper
- Thymopentin ameliorates experimental colitis via inhibiting neutrophil extracellular trapsInternational immunopharmacology · 2023
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 GSE223224_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 PRJNA925430 and SRA study SRP418245. 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.
- GSM6943618 TNB-N-1 TNB-N
- GSM6943619 TNB-N-2 TNB-N
- GSM6943620 TNB-N-3 TNB-N
- GSM6943621 TNB-T-1 TNB-T
- GSM6943622 TNB-T-2 TNB-T
- GSM6943623 TNB-T-3 TNB-T
- GSM6943624 DSS-N-1 DSS-N
- GSM6943625 DSS-N-2 DSS-N
- GSM6943626 DSS-N-3 DSS-N
- GSM6943627 DSS-T-1 DSS-T
- GSM6943628 DSS-T-2 DSS-T
- GSM6943629 DSS-T-3 DSS-T
- GSE272476 Neutrophils exposed to a cholesterol metabolite secrete extracellular vesicles that promote epithelial-mesenchymal transition and stemness in breast cancer cells [RNA-seq] 30 samples shares extracellular, neutrophil
- GSE284684 Peptidylarginine deiminase 4 deficiency improves elastase-induced formation of neutrophil extracellular traps and emphysema in mouse lung 24 samples shares extracellular, neutrophil
- GSE266962 Targeting Immunoproteasome in Macrophages Suppresses M1 Polarization and Ameliorates Experimental Emphysema via Activating NRF1 and NRF2-P62 Axis 24 samples shares experimental, ameliorates
- GSE254410 In the aftermath of stroke or myocardial infarction, neutrophil extracellular traps disrupt systemic immunoglobulin production 12 samples shares extracellular, neutrophil
- GSE298934 Activation of M3 muscarinic ameliorates experimental autoimmune encephalomyelitis by restoring microglial quiescence 9 samples shares experimental, ameliorates
- GSE243692 Small molecule probe for IBD risk variant GPR65 I231L alters cytokine signaling networks through positive allosteric modulation 90 samples shares ibd
- GSE207221 Claudin2 Upregulation: IBD and colitis-associated colon cancer 36 samples shares ibd
- GSE295428 Spaceflight induces systemic effects on extracellular matrix and immune system in different age-stages 229 samples shares extracellular
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.