RNA sequensing data of a phase 2 clinical trial of pancreatic ductal adenocarcinoma treated with entinostat in combination with nivolumab
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- Samples
- 45 samples: 45 samples, each with a distinct title — no replicated groupsGroups 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
- Entinostat in combination with nivolumab in metastatic pancreatic ductal adenocarcinoma: a phase 2 clinical trialNature 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 GSE248014_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 PRJNA1041407. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 45 sample titles: 45 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.
- GSM7904716 patient J1798_P28 at time point Baseline
- GSM7904717 patient J1798_P41 at time point Baseline
- GSM7904718 patient J1798_P41 at time point C1D1
- GSM7904719 patient J1798_P19 at time point Baseline
- GSM7904720 patient J1798_P19 at time point C1D1
- GSM7904721 patient J1798_P42 at time point Baseline
- GSM7904722 patient J1798_P8 at time point Baseline
- GSM7904723 patient J1798_P8 at time point C1D1
- GSM7904724 patient J1798_P5 at time point Baseline
- GSM7904725 patient J1798_P5 at time point C1D1
- GSM7904726 patient J1798_P1 at time point Baseline
- GSM7904727 patient J1798_P1 at time point C1D1
- GSM7904728 patient J1798_P27 at time point Baseline
- GSM7904729 patient J1798_P9 at time point Baseline
- GSM7904730 patient J1798_P40 at time point Baseline
- GSM7904731 patient J1798_P30 at time point Baseline
- GSM7904732 patient J1798_P24 at time point Baseline
- GSM7904733 patient J1798_P24 at time point C1D1
- GSM7904734 patient J1798_P34 at time point C1D1
- GSM7904735 patient J1798_P3 at time point Baseline
- GSM7904736 patient J1798_P3 at time point C1D1
- GSM7904737 patient J1798_P18 at time point Baseline
- GSM7904738 patient J1798_P18 at time point C1D1
- GSM7904739 patient J1798_P38 at time point Baseline
- GSM7904740 patient J1798_P38 at time point C1D1
- GSM7904741 patient J1798_P33 at time point Baseline
- GSM7904742 patient J1798_P33 at time point C1D1
- GSM7904743 patient J1798_P33 at time point C2D1
- GSM7904744 patient J1798_P44 at time point Baseline
- GSM7904745 patient J1798_P44 at time point C1D1
- GSM7904746 patient J1798_P44 at time point C2D1
- GSM7904747 patient J1798_P6 at time point C1D1
- GSM7904748 patient J1798_P14 at time point Baseline
- GSM7904749 patient J1798_P14 at time point C1D1
- GSM7904750 patient J1798_P26 at time point Baseline
- GSM7904751 patient J1798_P26 at time point C1D1
- GSM7904752 patient J1798_P15 at time point Baseline
- GSM7904753 patient J1798_P15 at time point C1D1
- GSM7904754 patient J1798_P15 at time point C2D1
- GSM7904755 patient J1798_P12 at time point Baseline
+ 5 more — browse all 45 samples with per-sample file links →
- GSE263733 Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications 218 samples shares adenocarcinoma, pancreatic, clinical
- GSE316195 A Phase 1 clinical trial and single-cell correlates of motixafortide, cemiplimab, gemcitabine and nab-paclitaxel for metastatic treatment-naïve metastatic pancreatic ductal adenocarcinoma. 22 samples shares adenocarcinoma, pancreatic, clinical
- GSE228801 Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction 14 samples shares adenocarcinoma, pancreatic, clinical
- GSE205154 Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks. 289 samples shares adenocarcinoma, pancreatic
- GSE310252 Transcriptome-based classification of resected pancreatic ductal adenocarcinoma enhances prognostic modelling accuracy of overall survival following adjuvant treatment 118 samples shares adenocarcinoma, pancreatic
- GSE288221 RNA sequencing human melanoma, glioblastoma and pancreatic adenocarcinoma cell lines 32 samples shares adenocarcinoma, pancreatic
- GSE254323 RNA-seq of colorectal cancer cell line HCT116 and DLD-1 cells treated with PRIMA-1met or oxaliplatin or combination therapy 24 samples shares combination, treated
- GSE318418 Immunosuppressive monocytes are enriched in hepatocellular carcinoma patients with liver dysfunction in a phase II trial of combination sorafenib and nivolumab [scRNA-Seq] 16 samples shares combination, nivolumab
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.