Bile acid synthesis impedes tumor-specific T cell responses during liver cancer [RNA-seq1]
RNA-seq (gene expression) · mouse · 24 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
- 24 samples: 8 conditions, mostly in triplicateGroups 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
- Bile acid synthesis impedes tumor-specific T cell responses during liver cancerScience (New York, N.Y.) · 2025
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 GSE279096_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 PRJNA1170414 and SRA study SRP537289. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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.
- GSM8561399 Control, replicate 1 Control,
- GSM8561400 Control, replicate 2 Control,
- GSM8561401 Control, replicate 3 Control,
- GSM8561402 LCA, replicate 1 LCA,
- GSM8561403 LCA, replicate 2 LCA,
- GSM8561404 LCA, replicate 3 LCA,
- GSM8561405 IsoAlloLCA, replicate 1 IsoAlloLCA,
- GSM8561406 IsoAlloLCA, replicate 2 IsoAlloLCA,
- GSM8561407 IsoAlloLCA, replicate 3 IsoAlloLCA,
- GSM8561408 IsoLCA, replicate 1 IsoLCA,
- GSM8561409 IsoLCA, replicate 2 IsoLCA,
- GSM8561410 IsoLCA, replicate 3 IsoLCA,
- GSM8561411 DehydroLCA, replicate 1 DehydroLCA,
- GSM8561412 DehydroLCA, replicate 2 DehydroLCA,
- GSM8561413 DehydroLCA, replicate 3 DehydroLCA,
- GSM8561414 TCA, replicate 1 TCA,
- GSM8561415 TCA, replicate 2 TCA,
- GSM8561416 TCA, replicate 3 TCA,
- GSM8561417 TCDCA, replicate 1 TCDCA,
- GSM8561418 TCDCA, replicate 2 TCDCA,
- GSM8561419 TCDCA, replicate 3 TCDCA,
- GSM8561420 UDCA, replicate 1 UDCA,
- GSM8561421 UDCA, replicate 2 UDCA,
- GSM8561422 UDCA, replicate 3 UDCA,
- GSE279097 Bile acid synthesis impedes tumor-specific T cell responses during liver cancer [RNA-seq2] 18 samples shares tumor-specific, synthesis, impedes, liver, bile, acid
- GSE279099 Bile acid synthesis impedes tumor-specific T cell responses during liver cancer. 48 samples shares tumor-specific, synthesis, impedes, liver, bile, acid
- GSE273290 Hepatic Lpcat3 Accelerates Nonalcoholic Fatty Liver Disease by slut1e1-related promoting fatty acid oxidation and reducing fatty acid synthesis [HFHS RNA-seq] 12 samples shares synthesis, liver, acid
- GSE273291 Hepatic Lpcat3 Accelerates Nonalcoholic Fatty Liver Disease by slut1e1-related promoting fatty acid oxidation and reducing fatty acid synthesis [MCD RNA-seq] 12 samples shares synthesis, liver, acid
- GSE288530 Microenvironmental arginine restriction sensitizes pancreatic cancers to polyunsaturated fatty acids by suppression of lipid synthesis 18 samples shares synthesis, acid
- GSE281057 Mitochondrial dysfunction enhances influenza pathogenesis by upregulating sialic acid biosynthesis 29 samples shares synthesis, acid
- GSE297103 Lysophosphatidic acid synergizes with 1,25-dihydroxyvitamin D to promote fibroblast growth factor-23 synthesis via MAPK signaling and induction of the IL12A gene 24 samples shares synthesis, acid
- GSE308565 SLC25A45 mediates mitochondrial import of methylated mitochondrial amino acids and carnitine biosynthesis 19 samples shares synthesis, acid
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.