mRNA/sRNA Co-Sequencing Reveals Multiple New Targeted Therapy Candidates in Rhabdomyosarcoma
RNA-seq (gene expression) · human · 26 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
- 26 samples: 4 × ARMS sample vs 4 × ERMS sample vs 3 × SCRMS sample vs 2 × Control sampleGroups 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.
Read the full summary ↓
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 GSE279954_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 PRJNA1175612 and SRA study SRP539879. 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 26 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.
- GSM8584139 ARMS sample 1 ARMS sample
- GSM8584140 ARMS samples 2
- GSM8584141 ARMS sample 5 ARMS sample
- GSM8584142 SCRMS sample 6 SCRMS sample
- GSM8584143 ERMS sample 7 ERMS sample
- GSM8584144 ARMS sample 8 ARMS sample
- GSM8584145 ERMS sample 9 ERMS sample
- GSM8584146 ERMS sample 10 ERMS sample
- GSM8584147 PRMS sample 11
- GSM8584148 ERMS sample 12 ERMS sample
- GSM8584149 ARMS sample 13 ARMS sample
- GSM8584150 SCRMS sample 14 SCRMS sample
- GSM8584151 SCRMS sample 15 SCRMS sample
- GSM8584152 control sample 17, WT counterpart to R_06T
- GSM8584153 Control sample 18, WT counterpart to R_14T
- GSM8584154 Control sample 19, WT counterpart to R_05T
- GSM8584155 Control sample 20 Control sample
- GSM8584156 Control sample 21, WT counterpart to R_11T
- GSM8584157 Control sample 22, WT counterpart to R_10T
- GSM8584158 Control sample 23 Control sample
- GSM8584159 Control sample 24, WT counterpart to R_12T
- GSM8584160 Control Sample 25, WT counterpart to R_15T
- GSM8584161 Control Sample 26, WT counterpart to R_13T
- GSM8584162 Control Sample 27, WT counterpart to R_02T
- GSM8584163 Control Sample 28, WT counterpart to R_02T
- GSM8584164 Control Sample 30
- GSE240287 RNA-sequencing of matched samples from rhabdomyosarcoma samples, obtained before therapy and mid-treatment resection 18 samples same disease briefing · shares rhabdomyosarcoma, therapy
- GSE274640 MYOD1L122R induces cancer stem cell pathways to impart chemotherapy and radiation-resistance in aggressive rhabdomyosarcoma. 80 samples same disease briefing · shares rhabdomyosarcoma, therapy
- 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
- GSE273829 GABA promotes resistance to immunotherapy of patients with TLS-positive tumors [RNA-seq] 92 samples same disease briefing · shares therapy
- GSE300974 CDK8 Inhibition Releases the Muscle Differentiation Blockade in Fusion-driven Alveolar Rhabdomyosarcoma [RNA-seq] 30 samples same disease briefing · shares rhabdomyosarcoma
- GSE314949 RNA Seq of rhabdomyosarcoma cells with sgRNA targeting oncofusion interacting proteins 30 samples same disease briefing · shares rhabdomyosarcoma
- GSE292872 FANCM is Required for the PAX3::FOXO1-Driven Oncogenic Program in Rhabdomyosarcoma [RNA-Seq] 21 samples same disease briefing · shares rhabdomyosarcoma
- GSE202614 TLE3 function in rhabdomyosarcoma tumor xenografts. 20 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.