RNA Seq of rhabdomyosarcoma cells with sgRNA targeting oncofusion interacting proteins
RNA-seq (gene expression) · human · 30 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
- Soft tissue sarcomaThis series is part of our curated briefing on it.
- Samples
- 30 samples: 10 conditions, mostly in triplicateGroups 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
- Fusion-positive rhabdomyosarcoma oncofusions share a common interactomeNature communications · 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 GSE314949_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 PRJNA1393393 and SRA study SRP657955. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 30 samples.
How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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.
- GSM9416825 sg Non-targeting control 1 sg Non-targeting control
- GSM9416826 sg Non-targeting control 2 sg Non-targeting control
- GSM9416827 sg Non-targeting control 3 sg Non-targeting control
- GSM9416828 sgFOXO1 1 sgFOXO1
- GSM9416829 sgFOXO1 2 sgFOXO1
- GSM9416830 sgFOXO1 3 sgFOXO1
- GSM9416831 sgNCOA1 1 sgNCOA1
- GSM9416832 sgNCOA1 2 sgNCOA1
- GSM9416833 sgNCOA1 3 sgNCOA1
- GSM9416834 sgNCOA2 1 sgNCOA2
- GSM9416835 sgNCOA2 2 sgNCOA2
- GSM9416836 sgNCOA2 3 sgNCOA2
- GSM9416837 sgINO80D 1 sgINO80D
- GSM9416838 sgINO80D 2 sgINO80D
- GSM9416839 sgINO80D 3 sgINO80D
- GSM9416840 sgMAML1 1 sgMAML1
- GSM9416841 sgMAML1 2 sgMAML1
- GSM9416842 sgMAML1 3 sgMAML1
- GSM9416843 sgINO80 1 sgINO80
- GSM9416844 sgINO80 2 sgINO80
- GSM9416845 sgINO80 3 sgINO80
- GSM9416846 sgTYMS 1 sgTYMS
- GSM9416847 sgTYMS 2 sgTYMS
- GSM9416848 sgTYMS 3 sgTYMS
- GSM9416849 sgWWTR1 1 sgWWTR1
- GSM9416850 sgWWTR1 2 sgWWTR1
- GSM9416851 sgWWTR1 3 sgWWTR1
- GSM9416852 sgHDAC2 1 sgHDAC2
- GSM9416853 sgHDAC2 2 sgHDAC2
- GSM9416854 sgHDAC2 3 sgHDAC2
- GSE332748 PAX3::FOXO1-Targeting PROTAC Induces Myogenic Differentiation of Fusion-Positive Rhabdomyosarcoma Cells 6 samples same disease briefing · shares rhabdomyosarcoma, targeting
- GSE275734 A multitargeting approach rewires cell identity in fusion-negative rhabdomyosarcoma [Human_RNAseq_bulk] 8 samples same disease briefing · shares rhabdomyosarcoma, targeting
- GSE279213 Targeting De Novo Cholesterol Synthesis as a Therapeutic Strategy in Rhabdomyosarcoma 8 samples same disease briefing · shares rhabdomyosarcoma, targeting
- GSE276201 A multitargeting approach rewires cell identity in fusion-negative rhabdomyosarcoma 28 samples same disease briefing · shares rhabdomyosarcoma, targeting
- GSE275736 A multitargeting approach rewires cell identity in fusion-negative rhabdomyosarcoma [bulk_ATACseq] 8 samples same disease briefing · shares rhabdomyosarcoma, targeting
- GSE282611 A multitargeting approach rewires cell identity in fusion-negative rhabdomyosarcoma [snRNAseq and scATACseq] 4 samples same disease briefing · shares rhabdomyosarcoma, targeting
- GSE312030 Combined inhibition of HRAS and MEK induces tumor regression and restores myogenic differentiation in HRAS-mutant rhabdomyosarcoma 159 samples same disease briefing · shares rhabdomyosarcoma
- GSE228127 Multimodal single-cell profiling reveals the enhanced antitumor activity of FGFR4/CD276 BiCisCAR T cells in rhabdomyosarcoma 12 samples same disease briefing · shares rhabdomyosarcoma
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.