Cholestasis-induced neutrophil phenotypic transformation contributes to the immune escape of colorectal liver metastasis
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 × neutrophil-PBS vs 3 × neutrophil-TCA vs 3 × neutrophil-TβMCA vs 3 × neutrophil-GCAGroups 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
- Cholestasis-induced phenotypic transformation of neutrophils contributes to immune escape of colorectal cancer liver metastasisJournal of biomedical science · 2024
Read the full summary ↓
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 GSE209836_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 PRJNA862549 and SRA study SRP388274. 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.
- GSM6401821 neutrophil-PBS-3 neutrophil-PBS
- GSM6401822 neutrophil-PBS-5 neutrophil-PBS
- GSM6401823 neutrophil-PBS-6 neutrophil-PBS
- GSM6401824 neutrophil-TCA-3 neutrophil-TCA
- GSM6401825 neutrophil-TCA-4 neutrophil-TCA
- GSM6401826 neutrophil-TCA-5 neutrophil-TCA
- GSM6401827 neutrophil-TβMCA-3 neutrophil-TβMCA
- GSM6401828 neutrophil-TβMCA-4 neutrophil-TβMCA
- GSM6401829 neutrophil-TβMCA-5 neutrophil-TβMCA
- GSM6401830 neutrophil-GCA-3 neutrophil-GCA
- GSM6401831 neutrophil-GCA-4 neutrophil-GCA
- GSM6401832 neutrophil-GCA-5 neutrophil-GCA
- GSE327176 Single-cell transcriptomic profiling unveils tumor-mediated reprogramming of neutrophils and their unique vulnerability that inhibits metastasis 25 samples shares neutrophil, metastasis
- GSE264607 Molecular targets of colorectal cancer transformation revealed by single-cell sequencing 14 samples shares transformation, colorectal
- GSE267535 TLR4-dependent fibroblast-monocyte axis in tumor-draining lymph nodes contributes to metastasis in triple-negative breast cancer 10 samples shares contributes, metastasis
- GSE300115 The Ly6Ghigh neutrophil subset occupying the early metastatic niche dictates breast cancer lung metastasis via cathelicidin-induced CD8+ T cell death_neutrophil 9 samples shares neutrophil, metastasis
- GSE329653 Flow induced-endothelial phenotypic transition contributes to Intracranial Aneurysm 9 samples shares contributes, phenotypic
- GSE278570 Neutrophils physically interact with tumor cells to form a signaling niche promoting breast cancer aggressiveness 309 samples shares neutrophil
- GSE301899 mTOR signaling contributes to system-driven rhythmic gene expression in mouse liver 282 samples shares contributes
- GSE198770 Circadian transcriptional profile of tissues with and without neutrophil depletion 191 samples shares neutrophil
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.