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
RNA-seq (gene expression) · human · 26 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
- 26 samples: 9 conditions, mostly in triplicateGroups 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
- Self-organization of sinusoidal vessels in pluripotent stem cell-derived human liver bud organoidsNature biomedical engineering · 2025
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 GSE217649_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 PRJNA899884 and SRA study SRP407061. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 25 samples.
How we read this: 9 replicated groups read from 26 sample titles; they account for 25 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.
- GSM6723964 iPSC_1 iPSC
- GSM6723965 iPSC_2 iPSC
- GSM6723966 iSTM_1 iSTM
- GSM6723967 iSTM_2 iSTM
- GSM6723968 iAEC_1 iAEC
- GSM6723969 iAEC_2 iAEC
- GSM6723970 iAEC_3 iAEC
- GSM6723971 iLSEP_1 iLSEP
- GSM6723972 iLSEP_2 iLSEP
- GSM6723973 iLSEP_3 iLSEP
- GSM6723974 Primary_LSEC_1
- GSM6723975 iLSEC_+VEGF+OSM_1 iLSEC_+VEGF+OSM
- GSM6723976 iLSEC_+VEGF+OSM_2 iLSEC_+VEGF+OSM
- GSM6723977 iLSEC_+VEGF+OSM_3 iLSEC_+VEGF+OSM
- GSM6723978 iLSEC_+VEGF_1 iLSEC_+VEGF
- GSM6723979 iLSEC_+VEGF_2 iLSEC_+VEGF
- GSM6723980 iLSEC_+VEGF_3 iLSEC_+VEGF
- GSM6723981 iAEC_HLBO_1 iAEC_HLBO
- GSM6723982 iAEC_HLBO_2 iAEC_HLBO
- GSM6723983 iAEC_HLBO_3 iAEC_HLBO
- GSM6723984 iLSEP_HLBO_1 iLSEP_HLBO
- GSM6723985 iLSEP_HLBO_2 iLSEP_HLBO
- GSM6723986 iLSEP_HLBO_3 iLSEP_HLBO
- GSM6723987 iHE_1 iHE
- GSM6723988 iHE_2 iHE
- GSM6723989 iHE_3 iHE
- GSE216842 Transcriptomic landscape of human primary stromal cells (fibroblasts, endothelial cells and mesenchymal stem cells) upon therapy-induced senescence (genotoxic chemotherapy） 24 samples shares endothelial, mesenchymal, primary
- GSE334500 Psychotropic-drug and neurotransmitter perturbation RNA-seq of human iPSC-derived cardiac and retinal organoids (ToxiPred) 96 samples shares ipsc-derived, organoids
- 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, organoids
- GSE296345 Paired-end RNA Sequencing on primary human umbilical endothelial cells (HUVEC) exposed to uninfected or bacterially-infected PMA-differentiated macrophage-like U937 for 8 or 24 h 24 samples shares endothelial, primary
- GSE237429 Single-cell transcriptomics reveals distinct molecular alterations of human renal cell carcinoma-derived endothelial cells that are stable in ex vivo primary culture 19 samples shares endothelial, primary
- GSE261696 Transcriptional characteristics of human primary, bone marrow-derived and iPSC-derived monocytes and macrophages [RNA-Seq] 19 samples shares ipsc-derived, primary
- GSE339602 Single-cell RNA sequencing of human iPSC-derived forebrain organoids following amyloid-β42 treatment, microglia co-culture, and maraviroc treatment 16 samples shares ipsc-derived, organoids
- GSE305558 Single-cell profiling reveals RAB13+ endothelial cells and profibrotic mesenchymal cells in aged human bone marrow 12 samples shares endothelial, mesenchymal
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.