Transcriptome analysis of primary human hepatocytes-derived organoids [RNA-seq]
RNA-seq (gene expression) · human · 82 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
- 82 samples: 82 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.
- Paper
- Generation of human adult hepatocyte organoids with metabolic functionsNature · 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 GSE228249_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 PRJNA949133 and SRA study SRP429470. 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 82 sample titles: 82 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.
- GSM7117688 PHH,PY39a,Female,39 yr. [R901]
- GSM7117689 PHH,PY53,Male,53 yr. [R1029]
- GSM7117690 PHH,PY61,Female,61 yr. [R1040]
- GSM7117691 PHH,PY61,Female,61 yr. [R1158]
- GSM7117692 PHH,PY63,Male,63 yr. [R1159]
- GSM7117693 PHH,PY39b,Female,39 yr. [R1160]
- GSM7117694 PHH,PY51,Male,51 yr. [R1161]
- GSM7117695 PHH,PM16,Male,16 mo. [R1206]
- GSM7117697 eHHO,PY61,Female,61 yr. [R1171]
- GSM7117698 eHHO,PY63,Male,63 yr. [R1191]
- GSM7117700 eHHO,PY39b,Female,39 yr. [R1181]
- GSM7117702 eHHO,PY51,Male,51 yr. [R1199]
- GSM7117705 eHHO,PM11,Male,11 mo. [R1385]
- GSM7117707 eHHO,PM16,Male,16 mo. [R1381]
- GSM7117709 eHHO,PY39a,Female,39 yr. [R1401]
- GSM7117712 eHHO,PY53,Male,53 yr. [R1405]
- GSM7117713 eHHO_dOSM,PY39a,Female,39 yr. [R1400]
- GSM7117714 eHHO_dOSM,PY53,Male,53 yr. [R1404]
- GSM7117715 eHHO_dOSM_dWR,PY39a,Female,39 yr. [R779]
- GSM7117716 eHHO_dOSM_dWR,PY53,Male,53 yr. [R1042]
- GSM7117717 dHHO,PY61,Female,61 yr. [R1162]
- GSM7117718 dHHO,PY63,Male,63 yr. [R1182]
- GSM7117719 dHHO,PY39b,Female,39 yr. [R1172]
- GSM7117720 dHHO,PY51,Male,51 yr. [R1192]
- GSM7117721 dHHO,PM16,Male,16 mo. [R1383]
- GSM7117722 dHHO,PM11,Male,11 mo. [R1387]
- GSM7117723 ICO,PY39a,Female,39 yr. [R1200]
- GSM7117724 ICO,PY39b,Female,39 yr. [R1202]
- GSM7117725 ICO,PY51,Male,51 yr. [R1204]
- GSM7117726 dHHO_dHC,PY61,Female,61 yr. [R1168]
- GSM7117727 dHHO_dHC,PY63,Male,63 yr. [R1188]
- GSM7117728 dHHO_dHC,PY39b,Female,39 yr. [R1178]
- GSM8496952 dHHO_WR,PY61,Female,61 yr. [R1163]
- GSM8496953 dHHO_WR,PY39b,Female,39 yr. [R1173]
- GSM8496954 dHHO_WR,PY63,Male,63 yr. [R1183]
- GSM8496955 eHHO_long,PY53,Male,53 yr. [R1369]
- GSM8496956 dHHO_long,PY53,Male,53 yr. [R1370]
- GSM8496957 eHHO_long,PY61,Female,61 yr. [R1371]
- GSM8496958 dHHO_long,PY61,Female,61 yr. [R1372]
- GSM8496959 eHHO_long,PY39b,Female,39 yr. [R1373]
+ 42 more — browse all 82 samples with per-sample file links →
- GSE274335 RNA-Seq analysis LPCAT3 knockdown effect on primary human endometrial stromal cells(HESC). 6 samples shares primary, rna-seq
- GSE205154 Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks. 289 samples shares primary, rna-seq
- GSE297742 Bulk RNA-seq of primary tumor biopsy samples from prostate adenocarcinoma patients 234 samples shares primary, rna-seq
- GSE342790 Development-inspired approach for the derivation of functional and transplantable salivary gland organoids from human pluripotent stem cells [RNA-Seq] 16 samples shares organoids, rna-seq
- GSE327289 Cerebrovascular Single-Nucleus RNA-Seq Reveals Heat Shock Activation and Vascular Remodeling in Alzheimer’s Disease and Primary Tauopathies 76 samples shares primary, rna-seq
- GSE294300 Single-cell gene expression profiles of cells from primary colorectal cancer and adjacent normal tissue [scRNA-Seq] 36 samples shares primary, rna-seq
- GSE337246 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scRNA-Seq organoids] 35 samples shares organoids, rna-seq
- GSE339484 RNA-seq profiling of 14 paired primary and recurrent glioma cases 28 samples shares primary, rna-seq
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.