Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 25 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- Gastric cancerThis series is part of our curated briefing on it.
- Samples
- 25 samples: 4 × ATAC YCC vs 4 × ATAC NCC vs 3 × ATAC SNU vs 2 × ATAC AGSGroups 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
- Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancerGenome research · 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 GSE264550_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1103134 and SRA study SRP503330. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 13 samples.
How we read this: 4 replicated groups read from 25 sample titles; they account for 13 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.
- GSM8219897 ATAC HS746T
- GSM8219898 ATAC LMSU
- GSM8219899 ATAC SH.10.TC
- GSM8219900 ATAC MKN1
- GSM8219901 ATAC GES1
- GSM8219902 ATAC NUGC3
- GSM8219903 ATAC NCC_STC_K140
- GSM8219904 ATAC YCC2 ATAC YCC
- GSM8219905 ATAC CLS145
- GSM8219906 ATAC YCC6 ATAC YCC
- GSM8219907 ATAC OCUM1
- GSM8219908 ATAC AGS ATAC AGS
- GSM8219909 ATAC GSU
- GSM8219910 ATAC IM95
- GSM8219911 ATAC KATOIII
- GSM8219912 ATAC NCC19 ATAC NCC
- GSM8219913 ATAC NCC20 ATAC NCC
- GSM8219914 ATAC NCC24 ATAC NCC
- GSM8219915 ATAC NCC59 ATAC NCC
- GSM8219916 ATAC SNU16 ATAC SNU
- GSM8219917 ATAC SNU1967 ATAC SNU
- GSM8219918 ATAC SNU719 ATAC SNU
- GSM8219919 ATAC YCC10 ATAC YCC
- GSM8219920 ATAC YCC21 ATAC YCC
- GSM8219921 ATAC AGS_r2 ATAC AGS
- GSE103045 Genetic and epigenetic gene inactivation coupling with KRAS activation in human gastric cancer [RNA-Seq] 3 samples same disease briefing · shares activation
- GSE13861 Gene expression signature-based novel prognostic risk score in gastric cancer 90 samples same disease briefing
- GSE134520 Dissecting the single-cell transcriptome network underlying gastric premalignant lesions and early gastric cancer [10x genomics] 13 samples same disease briefing
- GSE163558 Transcriptional heterogeneity in primary and metastatic gastric cancer revealed using single-cell RNA sequencing 10 samples same disease briefing
- GSE173195 Roles of LTBP1 in the gastric cancer cells 6 samples same disease briefing
- GSE182543 ALKBH5 cooperated with LINC00659 promote gastric cancer progression by JAK1 mRNA m6A-YTHDF2-dependent modification [polyA] 6 samples same disease briefing
- GSE119196 HOXC10 Overexpression Promotes Cell Proliferation and Migration through Regulation of CST1 Expression in Gastric Cancer 2 samples same disease briefing
- GSE171054 NINJ2 inhibition increased chemo-sensitivity by decreasing CICs in chemotherapy-resistant gastric cancer 2 samples same disease briefing
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.