Expression Analysis of 2D, 3D Quiescent, and 3D Activated Pancreatic Stellate Cells
RNA-seq (gene expression) · mouse · 8 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
- 8 samples: 8 samples, each with a distinct title — no replicated groupsGroups 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.
Read the full summary ↓
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 GSE93313_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 PRJNA360599 and SRA study SRP096327. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 8 sample titles: 8 distinct titles with little repetition. 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.
- GSM2450835 PSC4 2D
- GSM2450836 PSC5 2D
- GSM2450837 PSC4 3D
- GSM2450838 PSC5 3D
- GSM2450839 PSC4 T4 transwell coculture
- GSM2450840 PSC4 T5 transwell coculture
- GSM2450841 PSC5 T4 transwell coculture
- GSM2450842 PSC5 T5 transwell coculture
- GSE311286 Analysis of murine normal pancreatic organoids, pancreatitis-derived organoids, and PDAC organoids in complete media and of pancreatitis-derived organoids, and PDAC organoids cultured alone or cocultured with pancreatic stellate cells in reduced media 75 samples shares pancreatic, stellate
- GSE263080 RNA-sea of Smad4 wild-type or Smad4 knockout KPC PDAC organoids from monocultures or co-cultures with pancreatic stellate cells and RNA-seq of flow-sorted PSCs from the same co-cultures. 44 samples shares pancreatic, stellate
- GSE324779 Transcriptomic profiling of pancreatic stellate cells and pancreatic cancer cells in a gemcitabine-driven tumor-stroma supernatant transfer model 12 samples shares pancreatic, stellate
- GSE266918 RNA-seq expression analysis of liver, adipose, skeletal muscle, heart, and pancreatic islets from DO founder strain mice fed high-fat, high-sugar diet. [heart] 63 samples shares pancreatic
- GSE266923 RNA-seq expression analysis of liver, adipose, skeletal muscle, heart, and pancreatic islets from DO founder strain mice fed high-fat, high-sugar diet. [liver] 61 samples shares pancreatic
- GSE266920 RNA-seq expression analysis of liver, adipose, skeletal muscle, heart, and pancreatic islets from DO founder strain mice fed high-fat, high-sugar diet. [Adipose] 61 samples shares pancreatic
- GSE275728 Transcriptome analysis of pancreatic cancer cells with genetically modified Ptges or Ptger4 36 samples shares pancreatic
- GSE282210 Transcriptome analysis of quiescent livers and regenerating livers after partial hepatectomy (PH) in young and aged mice 133 samples shares quiescent
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.