RNA sequencing analysis of wild-type and ITF2357 or I-BET151 or JQ1 treated mouse pancreatic cancer KPC cells
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: 3 × Ctrl vs 3 × JQ1 vs 3 × I-BET151 vs 3 × ITF 2357Groups 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 GSE216552_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 PRJNA894206 and SRA study SRP404485. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM6679066 Ctrl 1 Ctrl
- GSM6679067 Ctrl 2 Ctrl
- GSM6679068 Ctrl 3 Ctrl
- GSM6679069 JQ1 1 JQ1
- GSM6679070 JQ1 2 JQ1
- GSM6679071 JQ1 3 JQ1
- GSM6679072 I-BET151 1 I-BET151
- GSM6679073 I-BET151 2 I-BET151
- GSM6679074 I-BET151 3 I-BET151
- GSM6679075 ITF 2357 1 ITF 2357
- GSM6679076 ITF 2357 2 ITF 2357
- GSM6679077 ITF 2357 3 ITF 2357
- 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 kpc, pancreatic, wild-type
- 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 kpc, pancreatic, wild-type
- GSE194370 RNAseq of 3 and 5 days differentiated C2C12 cells treated with conditioned medium of KPC, 4662, LLC or C26 cells 42 samples shares kpc, treated
- GSE254041 Depletion of PCCB and/or PIK3CA from pancreatic tumor cells KPC influences T cells infiltrating to TME 12 samples shares kpc, pancreatic
- 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 kpc, pancreatic
- GSE271510 Single-Cell RNA-Sequencing of Murine KPC Pancreatic Tumors 4 samples shares kpc, pancreatic
- GSE275876 Gene expression profile of Cd45 positive cells in single cell level from KRASLSL.G12D/+P53LSL.R172H/+Pdx-Cre mice (KPC tumor mouse) model treated with stimulator of interferon genes (STING) and lymphotoxin-beta receptor (LTbR) agonist [2024_v2] 4 samples shares kpc, treated
- GSE275840 Gene expression profile of Cd45 positive cells in single cell level from KRASLSL.G12D/+P53LSL.R172H/+Pdx-Cre mice (KPC tumor mouse) model treated with stimulator of interferon genes (STING) and lymphotoxin-beta receptor (LTbR) agonist 4 samples shares kpc, treated
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.