3D bioprinting of human liver models with biliary branching morphogenesis for hepatotoxicity, regeneration and NASH
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)
- Samples
- 12 samples: 3 × Model A vs 3 × Model B vs 3 × 2DD vs 3 × PHHGroups 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.
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 GSE205179_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 PRJNA844048 and SRA study SRP377793. 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.
- GSM6206872 Model A rep 1 Model A
- GSM6206873 Model A rep 2 Model A
- GSM6206874 Model A rep 3 Model A
- GSM6206875 Model B rep1 Model B
- GSM6206876 Model B rep2 Model B
- GSM6206877 Model B rep3 Model B
- GSM6206878 2DD rep1 2DD
- GSM6206879 2DD rep2 2DD
- GSM6206880 2DD rep3 2DD
- GSM6206881 PHH rep1 PHH
- GSM6206882 PHH rep2 PHH
- GSM6206883 PHH rep3 PHH
- GSE48452 Human liver biopsy of different phases from control to NASH 73 samples shares nash, liver
- GSE264357 Investigation of parenteral nutrition-induced hepatotoxicity using human liver spheroid co-cultures 12 samples shares hepatotoxicity, liver
- GSE298708 Three-Dimensional Bioprinted hiHeps Hepatorganoids with Improved Hepatic Functions for the Treatment of Acute / Chronic Liver failure and for the Promotion of Liver Regeneration 6 samples shares regeneration, liver
- GSE112713 Normothermic machine perfusion (NMP) inhibits proinflammatory responses in the liver and promotes regeneration 48 samples shares regeneration, liver
- GSE281574 Dysregulated RNA splicing induces regeneration failure in alcohol-associated liver disease 12 samples shares regeneration, liver
- GSE247467 Transcriptomic characterization of circulating neutrophils isolated from patients with metabolic dysfunction-associated steatohepatitis (MASH), formerly known as nonalcoholic steatohepatitis (NASH). 12 samples shares nash
- GSE292970 Spatially organizing million callus cells identify the core-network enable tomato shoot regeneration [RNA-Seq] 54 samples shares regeneration
- GSE278641 Growth signaling promotes H2A.Z deposition by SRCAP to sustain somatic tissue regeneration [RNA-Seq] 42 samples shares regeneration
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.