RNA sequencing data of primary cancer-associated fibroblasts (CAF) isolated from fresh ex vivo germ cell tumor (GCT) patient tissue
RNA-seq (gene expression) · human · 19 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
- Homo sapiens (human)
- Topic
- Testicular cancerThis series is part of our curated briefing on it.
- Samples
- 19 samples: 6 × SE-CAF vs 3 × EC-CAF vs 3 × TE-CAF vs 2 × Mix-CAFGroups 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
- Molecular and epigenetic ex vivo profiling of testis cancer-associated fibroblasts and their interaction with germ cell tumor cells and macrophagesMatrix biology : journal of the International Society for Matrix Biology · 2024
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 GSE229047_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 PRJNA952637 and SRA study SRP431142. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 4 replicated groups read from 19 sample titles; they account for 14 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.
- GSM7148330 SE-CAF009 SE-CAF
- GSM7148331 SE-CAF011 SE-CAF
- GSM7148332 SE-CAF018 SE-CAF
- GSM7148333 SE-CAF020 SE-CAF
- GSM7148334 SE-CAF021 SE-CAF
- GSM7148335 SE-CAF022 SE-CAF
- GSM7148336 EC-CAF005 EC-CAF
- GSM7148337 EC-CAF010 EC-CAF
- GSM7148338 EC-CAF014 EC-CAF
- GSM7148339 TE-CAF012 TE-CAF
- GSM7148340 TE-CAF017 TE-CAF
- GSM7148341 TE-CAF019 TE-CAF
- GSM7148342 Mix-CAF007 Mix-CAF
- GSM7148343 Mix-CAF008 Mix-CAF
- GSM7148344 nF-MPAF
- GSM7148345 nF-LB-C18m
- GSM7148346 nF-LB-35m
- GSM7148347 nF-LB-C2-36m
- GSM7148348 nF-iLB-C1-30m
- GSE278498 Refractory testicular germ cell tumors are highly sensitive to the targeting of polycomb pathway demethylases KDM6A and KDM6B 36 samples same disease briefing
- GSE317098 Comparative analysis of the transcriptomic response to cisplatin in drug-sensitive and drug-resistant testicular germ cell tumors. 30 samples same disease briefing
- GSE262137 Perfluorooctanesulfonic acid alters pro-cancer phenotypes and metabolic and transcriptional signatures in testicula germ cell tumors 26 samples same disease briefing
- GSE232791 Role of MIR9-2 in testicular germ cell tumours 16 samples same disease briefing
- GSE282367 BRD9 inhibition as potential treatment option for testicular germ cell tumors 12 samples same disease briefing
- GSE197778 Single-cell RNA sequencing of metastatic testicular seminoma reveals the cellular and molecular characteristics of metastatic cell lineage 4 samples same disease briefing
- GSE228501 Single-cell Multi-omics Analysis of Human Testicular Germ Cell Tumor Reveals its Molecular Features and Microenvironment 4 samples same disease briefing
- GSE261811 T cells in testicular germ cell tumors: new evidence of fundamental contributions by rare subsets 4 samples same disease briefing
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.