Analysis of human liver transcriptome after exposure to okadaic acid
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 × solvent control vs 3 × 11 nM OA vs 3 × 33 nM OA vs 3 × 100 nM OAGroups 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
- A multi-omics approach to elucidate okadaic acid-induced changes in human HepaRG hepatocarcinoma cellsArchives of toxicology · 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 GSE252563_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 PRJNA1061190 and SRA study SRP481834. 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.
- GSM8003279 solvent control_rep1 solvent control
- GSM8003280 solvent control_rep2 solvent control
- GSM8003281 solvent control_rep3 solvent control
- GSM8003282 11 nM OA_rep1 11 nM OA
- GSM8003283 11 nM OA_rep2 11 nM OA
- GSM8003284 11 nM OA_rep3 11 nM OA
- GSM8003285 33 nM OA_rep1 33 nM OA
- GSM8003286 33 nM OA_rep2 33 nM OA
- GSM8003287 33 nM OA_rep3 33 nM OA
- GSM8003288 100 nM OA_rep1 100 nM OA
- GSM8003289 100 nM OA_rep2 100 nM OA
- GSM8003290 100 nM OA_rep3 100 nM OA
- 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
- GSE167523 Transcriptome profiling of human non-alcoholic fatty liver disease 98 samples shares liver
- GSE251807 Investigation of gene expression changes in normal human dermal fibroblasts after exposure to bone marrow mesenchymal stromal cell secretome 32 samples shares exposure
- GSE319253 Eicosapentaenoic Acid Reprograms Cerebrovascular Metabolism and Impairs Repair after Brain Injury, with Relevance to Chronic Traumatic Encephalopathy [human_brain_OnurE_RNA-seq] 24 samples shares acid
- GSE304352 Transcriptome analysis of liver tissue from patients with Autoimmune Hepatitis, Primary Biliary Cholangitis, and Chronic Hepatitis B 11 samples shares liver
- GSE221608 Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participants of CRC 52 samples shares liver
- GSE276531 Hypothermic oxygenated machine perfusion influences the immunogenicity of donor livers in humans 32 samples shares liver
- GSE135251 TRANSCRIPTOMIC PROFILING ACROSS THE SPECTRUM OF NON-ALCOHOLIC FATTY LIVER DISEASE 216 samples shares liver
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.