Patient-derived organoid cultures model human primary liver cancer in vitro
RNA-seq (gene expression) · human · 59 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)
- Samples
- 59 samples: 59 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE84073_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 PRJNA327939 and SRA study SRP077971. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 59 sample titles: 59 distinct titles with little repetition. 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.
- GSM2653819 Healthy1-Tissue_1 [RNA-Seq]
- GSM2653820 Healthy1-Tissue_2 [RNA-Seq]
- GSM2653821 Healthy2-Tissue [RNA-Seq]
- GSM2653822 Healthy3-Tissue [RNA-Seq]
- GSM2653823 HCC1-Tissue_1 [RNA-Seq]
- GSM2653824 HCC1-Tissue_2 [RNA-Seq]
- GSM2653825 HCC3-Tissue [RNA-Seq]
- GSM2653826 CHC1-Tissue_1 [RNA-Seq]
- GSM2653827 CHC1-Tissue_2 [RNA-Seq]
- GSM2653828 CHC2-Tissue [RNA-Seq]
- GSM2653829 CC1-Tissue_1 [RNA-Seq]
- GSM2653830 CC1-Tissue_2 [RNA-Seq]
- GSM2653831 CC2-Tissue [RNA-Seq]
- GSM2653832 CC3-Tissue [RNA-Seq]
- GSM2653833 Healthy1-Organoid_1 [RNA-Seq]
- GSM2653834 Healthy1-Organoid_2 [RNA-Seq]
- GSM2653835 Healthy2-Organoid [RNA-Seq]
- GSM2653836 Healthy2-Organoid-DM [RNA-Seq]
- GSM2653837 Healthy3-Organoid [RNA-Seq]
- GSM2653838 Healthy3-Organoid-DM [RNA-Seq]
- GSM2653839 HCC1-Organoid_1 [RNA-Seq]
- GSM2653840 HCC1-Organoid_2 [RNA-Seq]
- GSM2653841 HCC3-Organoid [RNA-Seq]
- GSM2653842 CHC1-Organoid_1 [RNA-Seq]
- GSM2653843 CHC1-Organoid_2 [RNA-Seq]
- GSM2653844 CHC1-Organoid_a [RNA-Seq]
- GSM2653845 CHC1-Organoid_b [RNA-Seq]
- GSM2653846 CHC2-Organoid [RNA-Seq]
- GSM2653847 CC1-Organoid_1 [RNA-Seq]
- GSM2653848 CC1-Organoid_2 [RNA-Seq]
- GSM2653849 CC1-Organoid_a [RNA-Seq]
- GSM2653850 CC1-Organoid_b [RNA-Seq]
- GSM2653851 CC1-Organoid_c [RNA-Seq]
- GSM2653852 CC2-Organoid [RNA-Seq]
- GSM2653853 CC3-Organoid [RNA-Seq]
- GSM2653854 HCC1-Tissue [WES]
- GSM2653855 HCC3-Tissue [WES]
- GSM2653856 CHC1-Tissue [WES]
- GSM2653857 CHC2-Tissue [WES]
- GSM2653858 CC1-Tissue [WES]
+ 19 more — browse all 59 samples with per-sample file links →
- GSE217649 Bulk RNA sequencing for gene expression profileing of primary liver sinusoidal endothelial cells and iPSC-derived hepatic endoderm, septum mesenchymal cells, endothelial cells, and liver bud organoids 26 samples shares organoid, primary, liver
- GSE241466 Transcriptomic profiling of the intermediate cell carcinoma of the primary liver cancer 25 samples shares primary, liver
- GSE315534 Single-cell RNA sequencing of primary colorectal cancer, matched adjacent normal tissues, and paired liver metastases 15 samples shares primary, liver
- GSE303509 Biomarker-guided responses in patient-derived organoids predict effective therapies in breast cancer 14 samples shares patient-derived, organoid
- GSE221608 Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participants of CRC 52 samples shares primary, liver
- GSE263588 Comprehensive transcriptomic profiling of glioblastoma patient-derived primary tumor cell lines using bulk RNA-sequencing 49 samples shares patient-derived, primary
- GSE298576 Mass generation and long-term expansion of hepatocyte organoids from adult primary hepatocytes 24 samples shares organoid, primary
- GSE228801 Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction 14 samples shares patient-derived, organoid
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.