Differential Activity of MAPK signalling Defines Fibroblast Subtypes in Pancreatic Cancer
RNA-seq (gene expression) · mouse · 45 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
- 45 samples: 40 distinct titles, 3 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.
- Paper
- Differential activity of MAPK signalling defines fibroblast subtypes in pancreatic cancerNature communications · 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 GSE246459_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 PRJNA1032959 and SRA study SRP468892. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 4 samples read as cases, 12 as controls.
How we read this: Read from 45 sample titles: 40 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.
- GSM7869182 VR02-2D
- GSM7869183 VR06-2D
- GSM7869184 VR09-2D
- GSM7869185 VR20-2D
- GSM7869186 VR23-2D
- GSM7869205 PSC_NT_A_rep1
- GSM7869206 PSC_NT_A_rep2
- GSM7869207 PSC_TGFB_A_rep1
- GSM7869208 PSC_TGFB_A_rep2
- GSM7869209 PSC_TGFB_A_rep3
- GSM7869210 PSC_TGFB_A_rep4
- GSM7869219 PSC_NT_B_rep1
- GSM7869220 PSC_NT_B_rep2
- GSM7869229 vehichle,_treated, 2d, scRNAseq
- GSM7869230 Meki,_treated, 2d, scRNAseq
- GSM7869231 vehichle,_treated, 7d, scRNAseq
- GSM7869232 Meki,_treated, 7d, scRNAseq
- GSM8454387 PDAC1_A1
- GSM8454388 PDAC2_B1
- GSM8454389 PDAC3_C1
- GSM8454390 PDAC4_D1
- GSM8454744 Aspc1_MEKi
- GSM8454745 Aspc1_vehicle
- GSM8454746 Bxpc3_MEKi
- GSM8454747 Bxpc3_vehicle
- GSM8454748 Colo357_MEKi
- GSM8454749 Colo357_vehicle
- GSM8454750 hF2_MEKi
- GSM8454751 hF2_vehicle
- GSM8454752 Hpaf_II_MEKi
- GSM8454753 Hpaf_II_vehicle
- GSM8454754 Hs766t_Meki
- GSM8454755 Hs766t_vehicle
- GSM8454756 Miapaca_MEKi
- GSM8454757 Miapaca_vehicle
- GSM8454758 Panc1_MEKi
- GSM8454759 Panc1_vehicle
- GSM8454760 Patus_8988s_MEKi
- GSM8454761 Patus_8988s_vehicle
- GSM8454762 Suit2_MEKi
+ 5 more — browse all 45 samples with per-sample file links →
- GSE113616 Stromal Fibroblasts Drive Single Cell Heterogeneity in Pancreatic Cancer 189 samples same disease briefing · shares fibroblast, pancreatic
- GSE71729 Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes. 357 samples same disease briefing · shares pancreatic, subtypes
- GSE149250 Pancreatic Ductal Adenocarcinoma methylome analysis identifies differentially methylated genes in the Calcium signaling pathway and early methylation alterations. 15 samples same disease briefing · shares differential, pancreatic
- GSE143584 Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis 366 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
- 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
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.