Transcriptomic analysis of pathway activation after decitabine treatment in EBV+ vs EBV- gastric cancer [RNA-Seq]
RNA-seq (gene expression) · human · 20 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)
- Topic
- Gastric cancerThis series is part of our curated briefing on it.
- Samples
- 20 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.
- Paper
- Integrated transcriptomic and methylome analysis reveals retinoic acid pathway activation after decitabine treatment in EBV-associated gastric cancermBio · 2026
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 GSE309938_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 PRJNA1364017 and SRA study SRP644777. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 20 sample titles; they account for 20 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.
- GSM9285008 YCCEL1 cells, DMSO_rep1 YCCEL1 cells, DMSO
- GSM9285009 YCCEL1 cells, DMSO_rep2 YCCEL1 cells, DMSO
- GSM9285010 YCCEL1 cells, DCB_rep1 YCCEL1 cells, DCB
- GSM9285011 YCCEL1 cells, DCB_rep2 YCCEL1 cells, DCB
- GSM9285012 SNU719 cells, DMSO_rep1 SNU719 cells, DMSO
- GSM9285013 SNU719 cells, DMSO_rep2 SNU719 cells, DMSO
- GSM9285014 SNU719 cells, DCB_rep1 SNU719 cells, DCB
- GSM9285015 SNU719 cells, DCB_rep2 SNU719 cells, DCB
- GSM9285016 AGS cells, DMSO_rep1 AGS cells, DMSO
- GSM9285017 AGS cells, DMSO_rep2 AGS cells, DMSO
- GSM9285018 AGS cells, DCB_rep1 AGS cells, DCB
- GSM9285019 AGS cells, DCB_rep2 AGS cells, DCB
- GSM9285020 SNU16 cells, DMSO_rep1 SNU16 cells, DMSO
- GSM9285021 SNU16 cells, DMSO_rep2 SNU16 cells, DMSO
- GSM9285022 SNU16 cells, DCB_rep1 SNU16 cells, DCB
- GSM9285023 SNU16 cells, DCB_rep2 SNU16 cells, DCB
- GSM9285024 HGC27 cells, DMSO_rep1 HGC27 cells, DMSO
- GSM9285025 HGC27 cells, DMSO_rep2 HGC27 cells, DMSO
- GSM9285026 HGC27 cells, DCB_rep1 HGC27 cells, DCB
- GSM9285027 HGC27 cells, DCB_rep2 HGC27 cells, DCB
- GSE103045 Genetic and epigenetic gene inactivation coupling with KRAS activation in human gastric cancer [RNA-Seq] 3 samples same disease briefing · shares activation, gastric, rna-seq
- GSE173219 High-throughput sequencing of oxidative stress for Human gastric cancer cell lines treatment with Bioactive polypeptide chelating selenium (ACBP-S-Se) 2 samples same disease briefing · shares treatment, gastric
- GSE167297 Spatially distinct reprogramming of the tumor microenvironment based on tumor invasion in diffuse-type gastric cancers 14 samples same disease briefing · shares gastric
- GSE134520 Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer [10x genomics] 13 samples same disease briefing · shares gastric
- GSE163558 Transcriptional heterogeneity in primary and metastatic gastric cancer revealed using single-cell RNA sequencing 10 samples same disease briefing · shares gastric
- GSE173195 Roles of LTBP1 in the gastric cancer cells 6 samples same disease briefing · shares gastric
- GSE182543 ALKBH5 cooperated with LINC00659 promote gastric cancer progression by JAK1 mRNA m6A-YTHDF2-dependent modification [polyA] 6 samples same disease briefing · shares gastric
- GSE119196 HOXC10 Overexpression Promotes Cell Proliferation and Migration through Regulation of CST1 Expression in Gastric Cancer 2 samples same disease briefing · shares gastric
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.