Reprogramming of normal fibroblasts into ovarian cancer-associated fibroblasts via non-vesicular paracrine signaling induces an activated fibroblast phenotype
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Topic
- Ovarian cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × Primary CAF, vs 3 × Kuramochi CAF, vs 3 × Normal HUF, vs 3 × SKOV3 CAF,Groups 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
- Reprogramming of normal fibroblasts into ovarian cancer-associated fibroblasts via non-vesicular paracrine signaling induces an activated fibroblast phenotypeBiochimica et biophysica acta. Molecular cell research · 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 GSE280564_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 PRJNA1179415 and SRA study SRP541917. 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.
- GSM8600790 Primary CAF, rep 1 Primary CAF,
- GSM8600791 Primary CAF, rep 2 Primary CAF,
- GSM8600792 Primary CAF, rep 3 Primary CAF,
- GSM8600793 Kuramochi CAF, rep 1 Kuramochi CAF,
- GSM8600794 Kuramochi CAF, rep 2 Kuramochi CAF,
- GSM8600795 Kuramochi CAF, rep 3 Kuramochi CAF,
- GSM8600796 Normal HUF, rep 1 Normal HUF,
- GSM8600797 Normal HUF, rep 2 Normal HUF,
- GSM8600798 Normal HUF, rep 3 Normal HUF,
- GSM8600799 SKOV3 CAF, rep 1 SKOV3 CAF,
- GSM8600800 SKOV3 CAF, rep 2 SKOV3 CAF,
- GSM8600801 SKOV3 CAF, rep 3 SKOV3 CAF,
- GSE268514 Integrative genomic analysis of Korean high-grade serous ovarian cancer 161 samples same disease briefing
- GSE311212 Transcriptomic profiling in human ovarian cancer cell line OVCAR-3 following CDK2 inhibitor treatment 6 samples same disease briefing
- GSE154600 Multi-omic analysis of subtype evolution and heterogeneity in high-grade serous ovarian carcinoma 5 samples same disease briefing
- GSE128098 TET1 reprograms the epithelial ovarian cancer epigenome and reveals casein kinase 2α as a therapeutic target 4 samples same disease briefing
- GSE28330 Telomeric Allelic Imbalance Indicates Defective DNA Repair and Sensitivity to DNA-Damaging Agents 107 samples same disease briefing
- GSE57477 Molecular subtyping of serous ovarian tumors reveals multiple connections to intrinsic breast cancer subtypes 72 samples same disease briefing
- GSE314300 Rb CUT&RUN profiling in ovarian cancer cell lines following CDK2 inhibitor treatment 10 samples same disease briefing
- GSE135242 Hi-C identifies structural variation associated with resistance in paired patient-derived ovarian cancer models 8 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.