Epigenomic analysis of organoids from colorectal cancer peritoneal and liver metastases uncovers a mechanism of resistance to doxorubicin
RNA-seq (gene expression) · human · 15 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
- Colorectal cancerThis series is part of our curated briefing on it.
- Samples
- 15 samples
- 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.
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 GSE294934_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 PRJNA1252061 and SRA study SRP579449. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run HO176 … HO127 and carry no group information.
- GSM8930791 HO176
- GSM8930792 HO178
- GSM8930793 HO179
- GSM8930794 HO195
- GSM8930795 HO196
- GSM8930797 HO197
- GSM8930798 HO198
- GSM8930799 HO199
- GSM8930800 HO211
- GSM8930801 HO12
- GSM8930802 HO46
- GSM8930803 HO90
- GSM8930804 HO98
- GSM8930805 HO123
- GSM8930806 HO127
- GSE250000 Bulk RNA-sequencing of transduced colorectal cancer cell line HCT-116 and breast cancer cell line MCF-7 overexpressing full-lenght p53β or p53β-stop-lost. 4 samples same disease briefing · shares colorectal
- GSE12032 Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence 198 samples same disease briefing · shares colorectal
- GSE109308 Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations 97 samples same disease briefing
- GSE110009 Single cell transcriptome landscape of primary and metastatic tumor in colon cancer 76 samples same disease briefing
- GSE330465 Gene expression profiling of neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastases 104 samples shares colorectal, metastases
- GSE225182 Gene expression profiling study to identify distinct subtypes in Peritoneal metastasis of colorectal cancer 33 samples shares colorectal, peritoneal
- GSE289766 Analysis of the mechanism of acquisition of chemotherapy resistance in colorectal cancer cell lines 27 samples shares colorectal, resistance
- GSE310664 Analysis of experimental colorectal liver metastases identifies distinct proliferation independent transcriptional programs in micro- versus macrometastases 22 samples shares colorectal, metastases
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.