Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (RNA-Seq)
RNA-seq (gene expression) · human · 10 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
- 10 samples: 5 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.
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 GSE241926_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 PRJNA1010764 and SRA study SRP457572. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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.
- GSM7745717 GIST-T1, control, rep1 GIST-T1, control,
- GSM7745718 GIST-T1, InsE, rep1 GIST-T1, InsE,
- GSM7745719 GIST-T1, InsF, rep1 GIST-T1, InsF,
- GSM7745720 GIST-T1, InsG, rep1 GIST-T1, InsG,
- GSM7745721 GIST-T1, InsH, rep1 GIST-T1, InsH,
- GSM7745722 GIST-T1, control, rep2 GIST-T1, control,
- GSM7745723 GIST-T1, InsE, rep2 GIST-T1, InsE,
- GSM7745724 GIST-T1, InsF, rep2 GIST-T1, InsF,
- GSM7745725 GIST-T1, InsG, rep2 GIST-T1, InsG,
- GSM7745726 GIST-T1, InsH, rep2 GIST-T1, InsH,
- GSE241924 Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (ChIP-Seq) 45 samples same disease briefing · shares ctcf, gastrointestinal, dissection, chromosome, insulator, topology, oncogene, stromal
- GSE289088 Dual Role of IL-6 in Maintaining the resistance of Gastrointestinal stromal tumor and tumor angiogenesis 12 samples same disease briefing · shares gastrointestinal, stromal
- GSE254762 Deciphering the Tumor Immune Microenvironment of Imatinib-Resistance in Advanced Gastrointestinal Stromal Tumors at Single-Cell Resolution 9 samples same disease briefing · shares gastrointestinal, stromal
- 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 gastrointestinal, stromal
- 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 gastrointestinal, stromal
- GSE304624 Establishment of Patient-Derived Succinate Dehydrogenase-Deficient Gastrointestinal Stromal Tumor Models for Predicting Therapeutic Response 6 samples same disease briefing · shares gastrointestinal, stromal
- GSE240411 Identification of potential targets of FTO in GIST via transcriptome-wide RNA-seq 24 samples same disease briefing
- GSE282434 Effect of SHP2 Inhibition on mRNA Expression Profiles of GIST Cells 18 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.