RNA Sequencing Analysis of PFAS Impact on Liver Organoids
RNA-seq (gene expression) · human · 9 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
- 9 samples: 3 × PFOA vs 3 × PFUnDAGroups 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 GSE301790_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 PRJNA1287570 and SRA study SRP598879. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 6 samples.
How we read this: 2 replicated groups read from 9 sample titles; they account for 6 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.
- GSM9089821 DMSO-1.
- GSM9089822 DMSO-2.
- GSM9089823 DMSO-3.
- GSM9089824 PFOA-1 PFOA
- GSM9089825 PFOA-2 PFOA
- GSM9089826 PFOA-3 PFOA
- GSM9089827 PFUnDA-1 PFUnDA
- GSM9089828 PFUnDA-2 PFUnDA
- GSM9089829 PFUnDA-3 PFUnDA
- 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 organoids, liver
- GSE294934 Epigenomic analysis of organoids from colorectal cancer peritoneal and liver metastases uncovers a mechanism of resistance to doxorubicin 15 samples shares organoids, liver
- GSE322610 transcriptional analysis of unfrozen and cryopreserved liver organoids 12 samples shares organoids, liver
- GSE289912 APOE4 impacts cortical neurodevelopment and alters network formation in human brain organoids 32 samples shares organoids, impact
- GSE313992 Comparative Immunotoxicity and Transcriptomic Profiling of Seven PFAS in THP-1 Macrophages 252 samples shares pfas
- GSE263733 Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications 218 samples shares liver
- GSE244591 mRNA sequencing data of liver tumor tissues 136 samples shares liver
- GSE308421 Single-Cell RNA Sequencing Analysis of Intestinal organoids expanded in either IntestiCult™ Plus or IntestiCult™ OGM (Human) 10 samples shares organoids
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.