EGFR pathway regulates the cellular interactome within the liver fibrotic niche
RNA-seq (gene expression) · mouse · 15 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
- Mus musculus (mouse)
- Samples
- 15 samples
- 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
- The hepatocyte epidermal growth factor receptor (EGFR) pathway regulates the cellular interactome within the liver fibrotic nicheThe Journal of pathology · 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 GSE265969_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 PRJNA1105063 and SRA study SRP504222. Searching any of these in the dataset finder brings you back here.
The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Sample titles run AP7342 … AP7357 and carry no group information.
- GSM8238368 AP7342
- GSM8238369 AP7343
- GSM8238370 AP7344
- GSM8238371 AP7345
- GSM8238372 AP7346
- GSM8238373 AP7347
- GSM8238374 AP7348
- GSM8238375 AP7350
- GSM8238376 AP7351
- GSM8238377 AP7352
- GSM8238378 AP7353
- GSM8238379 AP7354
- GSM8238380 AP7355
- GSM8238381 AP7356
- GSM8238382 AP7357
- GSE276072 Gene expression profile at single cell level of mouse liver in whole and fibrotic niche of the liver 24 samples shares fibrotic, liver, niche
- GSE298799 Deconstructing the Intercellular Interactome in Vascular Dementia with Focal Ischemia for Therapeutic Applications 77 samples shares interactome, cellular
- GSE244429 BMP9 and BMP10 coordinate liver cellular crosstalk to maintain liver health 24 samples shares cellular, liver
- GSE327752 Human breast milk-derived extracellular vesicles alleviate Alzheimer’s disease phenotypes through delivering CD36 18 samples shares cellular, liver
- GSE230838 Loss of cisPTase function in the liver promotes a highly penetrant form of fatty liver disease that rapidly transitions to hepatocellular carcinoma [RNA-seq] 17 samples shares cellular, liver
- GSE261139 Tumour-derived Extracellular Vesicle and Particle Reprogramming of Interstitial Macrophages in the Lung Pre-Metastatic Niche Enhances Vascular Permeability and Metastatic Potential 16 samples shares cellular, niche
- GSE311064 Cellular senescence in human liver under normal aging and cancer 12 samples shares cellular, liver
- GSE314515 Static Magnetic Fields Exposure Allievates Liver Injury via Promoting Ca 2+ Influx and Cellular Respiration [scRNA-Seq] 8 samples shares cellular, 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.