Spatiotemporal control of SMARCA5 by a MAPK-RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration (RNA-Seq)
RNA-seq (gene expression) · mouse · 28 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)
- Topic
- Pancreatic cancerThis series is part of our curated briefing on it.
- Samples
- 28 samples: 10 conditions, mostly in duplicateGroups 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 GSE248947_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 PRJNA1046497 and SRA study SRP474954. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 4 as controls.
How we read this: 10 replicated groups read from 28 sample titles; they account for 23 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.
- GSM7923457 RNA_D7_Rosa_724 RNA_D7_Rosa
- GSM7923458 RNA_D7_Rosa_805 RNA_D7_Rosa
- GSM7923459 RNA_D7_Smarca5_722 RNA_D7_Smarca5
- GSM7923460 RNA_D7_Smarca5_770 RNA_D7_Smarca5
- GSM7923461 RNA_D7_Rosa_22 RNA_D7_Rosa
- GSM7923462 RNA_D7_Rosa_55 RNA_D7_Rosa
- GSM7923463 RNA_D7_Rosa_738 RNA_D7_Rosa
- GSM7923464 RNA_D7_Runx1_737 RNA_D7_Runx1
- GSM7923465 RNA_D7_Runx1_741 RNA_D7_Runx1
- GSM7923466 RNA_tumor_Rosa_953 RNA_tumor_Rosa
- GSM7923467 RNA_tumor_Rosa_993 RNA_tumor_Rosa
- GSM7923468 RNA_tumor_Smarca5_888 RNA_tumor_Smarca5
- GSM7923469 RNA_tumor_Smarca5_893 RNA_tumor_Smarca5
- GSM8795432 PDCC,shRUNX1,rep1 PDCC,shRUNX1,
- GSM8795433 PDCC,shRUNX1,rep2 PDCC,shRUNX1,
- GSM8795434 PDCC,shScramble,rep1 PDCC,shScramble,
- GSM8795435 PDCC,shScramble,rep2 PDCC,shScramble,
- GSM8795436 PDCC,shSMARCA5,rep1 PDCC,shSMARCA5,
- GSM8795437 PDCC,shSMARCA5,rep2 PDCC,shSMARCA5,
- GSM8795438 PDCC,DMSO,rep1 PDCC,DMSO,
- GSM8795439 PDCC,DMSO,rep2 PDCC,DMSO,
- GSM8795440 PDCC,GSK2801,rep1 PDCC,GSK2801,
- GSM8795441 PDCC,GSK2801,rep2 PDCC,GSK2801,
- GSM8795442 tumor,Rosa,211
- GSM8795443 tumor,Smarca5,212
- GSM8795444 D7,Rosa,33
- GSM8795445 D7,Runx1,27
- GSM8795446 D7,Smarca5,33
- GSE143584 Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis 366 samples same disease briefing · shares pancreatic
- GSE113616 Stromal Fibroblasts Drive Single Cell Heterogeneity in Pancreatic Cancer 189 samples same disease briefing · shares pancreatic
- GSE179351 Radiation Therapy Inhances Immunotherapy Response in Microsatellite-stable Colorectal and Pancreatic Adenocarcinoma in a Phase II Trial 54 samples same disease briefing · shares pancreatic
- GSE148188 NOXA dependent induction of apoptosis in pancreatic cancer cells 49 samples same disease briefing · shares pancreatic
- GSE273492 Selective NSD2 Inhibition Reveals an Epigenetic Vulnerability of KRAS-Driven Cancers [RNA-Seq] 36 samples same disease briefing · shares kras-driven
- GSE288221 RNA sequencing human melanoma, glioblastoma and pancreatic adenocarcinoma cell lines 32 samples same disease briefing · shares pancreatic
- GSE111672 Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas 23 samples same disease briefing · shares pancreatic
- GSE150043 Deeper insight into Pancreatic Ductal Adenocarcinoma (PDAC) survival heterogeneity using integrative analyses of individual and global transcriptome based networks 19 samples same disease briefing · shares pancreatic
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.