Gene expression profile at single cell level of immune cells and gastric cancer cells from multipoint biopsy samples of 2 gastric cancer patients treated by PD-1 antibody-based therapy
Single-cell RNA-seq · human · 12 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Topic
- Gastric cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 12 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.
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 GSE234209_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA980287 and SRA study SRP441250. 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 12 sample titles: 12 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.
- GSM7457272 P1ST_1, replicate 1, scRNAseq
- GSM7457273 P1PB_1, replicate 1, scRNAseq
- GSM7457274 P1AS_1, replicate 1, scRNAseq
- GSM7457275 P1PL_1, replicate 1, scRNAseq
- GSM7457276 P1PB_2, replicate 1, scRNAseq
- GSM7457277 P1PL_2, replicate 1, scRNAseq
- GSM7457278 P2ST_1, replicate 1, scRNAseq
- GSM7457279 P2PB_1, replicate 1, scRNAseq
- GSM7457280 P2AS_1, replicate 1, scRNAseq
- GSM7457281 P2ST_2, replicate 1, scRNAseq
- GSM7457282 P2PB_2, replicate 1, scRNAseq
- GSM7457283 P2AS_2, replicate 1, scRNAseq
- GSE171054 NINJ2 inhibition increased chemo-sensitivity by decreasing CICs in chemotherapy-resistant gastric cancer 2 samples same disease briefing · shares gastric, therapy
- 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
- GSE103045 Genetic and epigenetic gene inactivation coupling with KRAS activation in human gastric cancer [RNA-Seq] 3 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
- GSE182542 ALKBH5 cooperated with LINC00659 promote gastric cancer progression by JAK1 mRNA m6A-YTHDF2-dependent modification [2-m6A] 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.