Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistance [drug]
RNA-seq (gene expression) · mouse · 33 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
- 33 samples: 5 conditions, mostly with about 6 replicates eachGroups 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
- Adaptation to an acid microenvironment promotes pancreatic cancer organoid growth and drug resistanceCell reports · 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 GSE218177_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 PRJNA902680 and SRA study SRP408394. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 33 samples.
How we read this: 5 replicated groups read from 33 sample titles; they account for 33 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.
- GSM6736055 mP4_CTRL_Week1_Res1 mP4_CTRL_Week1_Res
- GSM6736056 mP4_CTRL_Week1_Res2 mP4_CTRL_Week1_Res
- GSM6736057 mP4_CTRL_Week1_Res3 mP4_CTRL_Week1_Res
- GSM6736058 mP4_CTRL_Week1_Res4 mP4_CTRL_Week1_Res
- GSM6736059 mP4_CTRL_Week1_Res5 mP4_CTRL_Week1_Res
- GSM6736060 mP4_CTRL_Week1_Res6 mP4_CTRL_Week1_Res
- GSM6736061 mP4_CTRL_Week1_Res7 mP4_CTRL_Week1_Res
- GSM6736062 mP4_CTRL_Week1_Res8 mP4_CTRL_Week1_Res
- GSM6736063 mP4_CTRL_Week1_Res9 mP4_CTRL_Week1_Res
- GSM6736064 mP4_CTRL_Week1_Res10 mP4_CTRL_Week1_Res
- GSM6736065 mP4_CTRL_Week1_Res11 mP4_CTRL_Week1_Res
- GSM6736066 mP4_CTRL_Week1_Res12 mP4_CTRL_Week1_Res
- GSM6736067 mP4_CTRL_Week12_Res25 mP4_CTRL_Week12_Res
- GSM6736068 mP4_CTRL_Week12_Res26 mP4_CTRL_Week12_Res
- GSM6736069 mP4_CTRL_Week12_Res27 mP4_CTRL_Week12_Res
- GSM6736070 mP4_E_Week12_Res28 mP4_E_Week12_Res
- GSM6736071 mP4_E_Week12_Res29 mP4_E_Week12_Res
- GSM6736072 mP4_E_Week12_Res30 mP4_E_Week12_Res
- GSM6736073 mP4_G_Week12_Res31 mP4_G_Week12_Res
- GSM6736074 mP4_G_Week12_Res32 mP4_G_Week12_Res
- GSM6736075 mP4_G_Week12_Res33 mP4_G_Week12_Res
- GSM6736076 mP4_E+G_Week12_Res34 mP4_E+G_Week12_Res
- GSM6736077 mP4_E+G_Week12_Res35 mP4_E+G_Week12_Res
- GSM6736078 mP4_E+G_Week12_Res36 mP4_E+G_Week12_Res
- GSM6736079 mP4_E_Week12_Res37 mP4_E_Week12_Res
- GSM6736080 mP4_E_Week12_Res38 mP4_E_Week12_Res
- GSM6736081 mP4_E_Week12_Res39 mP4_E_Week12_Res
- GSM6736082 mP4_G_Week12_Res40 mP4_G_Week12_Res
- GSM6736083 mP4_G_Week12_Res41 mP4_G_Week12_Res
- GSM6736084 mP4_G_Week12_Res42 mP4_G_Week12_Res
- GSM6736085 mP4_E+G_Week12_Res43 mP4_E+G_Week12_Res
- GSM6736086 mP4_E+G_Week12_Res44 mP4_E+G_Week12_Res
- GSM6736087 mP4_E+G_Week12_Res45 mP4_E+G_Week12_Res
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares pancreatic, resistance, promotes
- 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 pancreatic, organoid
- 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 pancreatic, organoid
- GSE292146 Tractable mouse TNBC models capture the heterogeneous tumor immune microenvironment and adaptation to PD-L1 blockade 38 samples shares microenvironment, adaptation
- 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 pancreatic, organoid
- GSE287625 Mitochondrial Ca2+ controls pancreatic cancer growth and metastasis by regulating epithelial cell plasticity 18 samples shares pancreatic, growth
- GSE269680 CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma (spatial) 15 samples shares microenvironment, pancreatic
- GSE241850 Psychological stress-induced ALKBH5 deficiency promotes tumour innervation and pancreatic cancer progression via extracellular vesicle transfer of m6A-modified RNAs 57 samples shares pancreatic, promotes
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.