Effect of SHP2 Inhibition on mRNA Expression Profiles of GIST Cells
RNA-seq (gene expression) · human · 18 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
- Gastrointestinal stromal tumourThis series is part of our curated briefing on it.
- Samples
- 18 samples: 18 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
- SHP2 inhibition and adjuvant therapy synergistically target KIT-mutant GISTs via ERK1/2-regulated GSK3β/cyclin D1 pathwayClinical and translational medicine · 2025
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 GSE282434_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 PRJNA1188572 and SRA study SRP546510. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 9 samples read as cases, 9 as controls.
How we read this: Read from 18 sample titles: 18 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.
- GSM8643071 GIST T1 cells, control, cultured for 24 hours [T1-ctrl-1]
- GSM8643072 GIST T1 cells, treated with SHP099 (20 µM) for 24 hours [T1-SHP099-1]
- GSM8643073 GIST T1/D816E cells, control, cultured for 24 hours [ctrl-816-1]
- GSM8643074 GIST T1/D816E cells, treated with SHP099 (20 µM) for 24 hours [SHP099-816-1]
- GSM8643075 GIST 430/V654A cells, control, cultured for 24 hours [ctrl-430-1]
- GSM8643076 GIST 430/V654A cells, treated with SHP099 (20 µM) for 24 hours [SHP099-430-1]
- GSM8643077 GIST T1 cells, control, cultured for 24 hours [T1-ctrl-2]
- GSM8643078 GIST T1 cells, treated with SHP099 (20 µM) for 24 hours [T1-SHP099-2]
- GSM8643079 GIST T1/D816E cells, control, cultured for 24 hours [ctrl-816-2]
- GSM8643080 GIST T1/D816E cells, treated with SHP099 (20 µM) for 24 hours [SHP099-816-2]
- GSM8643081 GIST 430/V654A cells, control, cultured for 24 hours [ctrl-430-2]
- GSM8643082 GIST 430/V654A cells, treated with SHP099 (20 µM) for 24 hours [SHP099-430-2]
- GSM8643083 GIST T1 cells, control, cultured for 24 hours [T1-ctrl-3]
- GSM8643084 GIST T1 cells, treated with SHP099 (20 µM) for 24 hours [T1-SHP099-3]
- GSM8643085 GIST T1/D816E cells, control, cultured for 24 hours [ctrl-816-3]
- GSM8643086 GIST T1/D816E cells, treated with SHP099 (20 µM) for 24 hours [SHP099-816-3]
- GSM8643087 GIST 430/V654A cells, control, cultured for 24 hours [ctrl-430-3]
- GSM8643088 GIST 430/V654A cells, treated with SHP099 (20 µM) for 24 hours [SHP099-430-3]
- GSE301351 The single-cell transcriptome defines an effector Vd1 gd T cell-dependent anti-tumor immunity in human gastrointestinal stromal tumor (GIST) [10X] 6 samples same disease briefing · shares gist
- GSE240411 Identification of potential targets of FTO in GIST via transcriptome-wide RNA-seq 24 samples same disease briefing · shares gist
- GSE296175 Claudin-1 contributes to gastrointestinal stromal tumors (GIST) resistance to imatinib mesylate (IM) via regulation of FGFR2-mediated signaling. 9 samples same disease briefing · shares gist
- GSE330412 Bulk RNA-sequencing after estrogen-related receptorr knockdown (ESRRA) knockdown in human GIST-T1 cell line 9 samples same disease briefing · shares gist
- GSE241926 Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (RNA-Seq) 10 samples same disease briefing
- GSE289088 Dual Role of IL-6 in Maintaining the resistance of Gastrointestinal stromal tumor and tumor angiogenesis 12 samples same disease briefing
- GSE254762 Deciphering the Tumor Immune Microenvironment of Imatinib-Resistance in Advanced Gastrointestinal Stromal Tumors at Single-Cell Resolution 9 samples same disease briefing
- GSE304624 Establishment of Patient-Derived Succinate Dehydrogenase-Deficient Gastrointestinal Stromal Tumor Models for Predicting Therapeutic Response 6 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.