A human iPSC-derived multilineage liver organoid model containing Kupffer cells to study human sepsis-associated liver dysfunction
RNA-seq (gene expression) · human · 22 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
- 22 samples: 10 conditions, mostly in duplicateGroups 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
- Integration of Kupffer cells into human iPSC-derived liver organoids for modeling liver dysfunction in sepsisCell reports · 2024
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 GSE233539_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 PRJNA976626 and SRA study SRP439606. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 10 replicated groups read from 22 sample titles; they account for 22 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.
- GSM7429227 KuLOs, Control, rep1 KuLOs, Control,
- GSM7429228 KuLOs, Control, rep2 KuLOs, Control,
- GSM7429229 KuLOs, septic, rep1 KuLOs, septic,
- GSM7429230 KuLOs, septic, rep2 KuLOs, septic,
- GSM7429231 KuLOs, recovery D1, rep1 KuLOs, recovery D1,
- GSM7429232 KuLOs, recovery D1, rep2 KuLOs, recovery D1,
- GSM7429233 KuLOs, recovery D2, rep1 KuLOs, recovery D2,
- GSM7429234 KuLOs, recovery D2, rep2 KuLOs, recovery D2,
- GSM7429235 KuLOs, recovery D3, rep1 KuLOs, recovery D3,
- GSM7429236 KuLOs, recovery D3, rep2 KuLOs, recovery D3,
- GSM7429955 hiPSC, rep1 hiPSC,
- GSM7429956 hiPSC, rep2 hiPSC,
- GSM7429957 hiPSC-EMP, rep1 hiPSC-EMP,
- GSM7429958 hiPSC-EMP, rep2 hiPSC-EMP,
- GSM7429959 CB-HSPC, rep1 CB-HSPC,
- GSM7429960 CB-HSPC, rep2 CB-HSPC,
- GSM7429961 EMP-KC, rep1 EMP-KC,
- GSM7429962 EMP-KC, rep2 EMP-KC,
- GSM7429963 EMP-KC, rep3 EMP-KC,
- GSM7429964 EMP-KC, rep4 EMP-KC,
- GSM7429965 primary KC, rep1 primary KC,
- GSM7429966 primary KC, rep2 primary KC,
- 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 ipsc-derived, organoid, liver
- GSE198888 Generation of 3D tubular bile duct within human iPSC-derived liver organoid by incorporating human iPSC-derived blood vessel [RNA-seq] 10 samples shares ipsc-derived, organoid, liver
- GSE334500 Psychotropic-drug and neurotransmitter perturbation RNA-seq of human iPSC-derived cardiac and retinal organoids (ToxiPred) 96 samples shares ipsc-derived, organoid
- GSE281797 Transcriptomic profiles of liver biopsies in obese patients with metabolic dysfunction-associated steatotic liver disease 94 samples shares dysfunction, liver
- GSE307755 Direct contact between iPSC-derived macrophages and hepatocytes drives reciprocal acquisition of Kupffer cell identity and hepatocyte maturation 53 samples shares ipsc-derived, kupffer
- GSE274114 Metabolic dysfunction-associated steatohepatitis reduces interferon and macrophage liver gene signatures in chronic HBV patients 39 samples shares dysfunction, liver
- GSE301365 Single-cell analysis of human iPSC-derived midbrain organoids generated with triphasic Wnt modulation combined with a dynamic bioreactor 30 samples shares ipsc-derived, organoid
- GSE266526 Device-free isolation of photoreceptor cells from patient iPSC-derived retinal organoids 19 samples shares ipsc-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.