Analysis of murine pancreatitis tissues and KPC PDAC tumours
RNA-seq (gene expression) · mouse · 13 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
- 13 samples: 12 distinct titles, 1 of them repeatedGroups 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 GSE311531_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 PRJNA1369607 and SRA study SRP649014. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 13 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.
- GSM9326599 P_67_35K
- GSM9326600 P_68_35K
- GSM9326601 P_64_70K_batch2
- GSM9326602 P_63_55K
- GSM9326603 P_63_70K
- GSM9326604 P_64_55K
- GSM9326605 P_62_70K
- GSM9326606 KPC_16.3b_35K
- GSM9326607 KPC_12.3b_35K
- GSM9326608 KPC_7.2b_35K
- GSM9326609 KPC_14.3f_35K
- GSM9326610 P_64_70K_batch4
- GSM9326611 P_65_70K
- 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, kpc
- GSE329665 Single-nuclei RNA-sequencing (snRNA-seq) of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 WT or Smad4 KO pancreatic ductal adenocarcinoma (PDAC) KPC (i.e. KrasG12D; p53 mutant) organoids in C57BL/6J mice. 6 samples shares pdac, kpc
- 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, kpc
- GSE274516 Combination of MEK and Autophagy Inhibition in the preclinical GEMM model of PDAC (KPC mice) 6 samples shares pdac, kpc
- GSE222133 CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub and H3K27me3 in treated KPC1199 murine PDAC cell line 12 samples shares pdac, kpc
- GSE246545 CUT&Tag analysis of H3K4me3 and Paxip1 in CRISPR/Cas9-mediated Paxip1 knockout KPC1199 murine PDAC cell line 12 samples shares pdac, kpc
- GSE229903 CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub, H3K27me3 and H3K36me3 in KPC1199 murine PDAC cell line 10 samples shares pdac, kpc
- GSE229051 ATAC-seq analysis in KPC1199 murine PDAC cell line with or without glutamine starvation 4 samples shares pdac, kpc
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.