Bulk RNA-sequencing analyses of multi-stroma flow-sorted from cocultures with murine pancreatitis (P)-derived organoids, PDAC organoids, or PDAC organoids following initial coculture with P organoids (ie P-to-PDAC or sequential).
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 12 samples: 12 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.
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 GSE329640_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 PRJNA1460364 and SRA study SRP696349. 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 12 sample titles: 12 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.
- GSM9708037 07_PSC5_FIBRO27_MG1
- GSM9708038 09_PSC5_FIBRO27_MG1
- GSM9708039 16_PSC4_FIBRO28_MH11
- GSM9708040 40_PSC4_FIBRO28_MH11
- GSM9708041 04_PSC4_FIBRO27_MH11
- GSM9708042 11_PSC5_FIBRO27_MG1
- GSM9708043 13_PSC5_FIBRO27_MG1
- GSM9708044 18_PSC4_FIBRO28_MH11
- GSM9708045 26_PSC4_FIBRO27_MH11
- GSM9708046 30_PSC4_FIBRO28_MH11
- GSM9708047 34_PSC5_FIBRO27_MG1
- GSM9708048 36_PSC5_FIBRO27_MG1
- 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 pdac, pancreatitis, organoids
- 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 pdac, flow-sorted, organoids
- GSE263081 RNA-sea of Smad4 wild-type or Smad4 knockout KvPC PDAC organoids from monocultures or co-cultures with pancreatic stellate cells and RNA-seq of flow-sorted PSCs from the same co-cultures. 35 samples shares pdac, flow-sorted, organoids
- GSE262879 Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KPC organoids in nu/nu mice. 18 samples shares pdac, rna-sequencing, organoids
- GSE262878 Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KvPC organoids in nu/nu mice 8 samples shares pdac, rna-sequencing, organoids
- GSE311531 Analysis of murine pancreatitis tissues and KPC PDAC tumours 13 samples shares pdac, pancreatitis
- GSE246251 Bulk RNA-sequencing of mouse prostate tumors initiated by transplantation of engineered organoids. 18 samples shares rna-sequencing, organoids
- GSE218337 Genotype-phenotype relationships (VPA/CHIR99021 vs. control; p53 Null vs. WT) in bulk RNA-sequencing of small intestinal murine organoids [bulk RNA-seq] 17 samples shares rna-sequencing, 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.