Single-cell RNA-sequencing of undifferentiated pleomorphic sarcoma, myxofibrosarcoma, and liposarcoma samples from patients participating in a clinical trial studying BO-112 plus Nivolumab and hypofractionated pre-operative radiotherapy.
Single-cell RNA-seq · human · 10 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
- Soft tissue sarcomaThis series is part of our curated briefing on it.
- Samples
- 10 samples: 10 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 GSE279852_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 PRJNA1174211. 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 10 sample titles: 10 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.
- GSM8581957 scRNA-seq of human soft tissue sarcoma sample - BO112-004-baseline
- GSM8581958 scRNA-seq of human soft tissue sarcoma sample - BO112-007-baseline
- GSM8581959 scRNA-seq of human soft tissue sarcoma sample - BO112-009-baseline
- GSM8581960 scRNA-seq of human soft tissue sarcoma sample - BO112-009-surgery
- GSM8581961 scRNA-seq of human soft tissue sarcoma sample - BO112-010-baseline
- GSM8581962 scRNA-seq of human soft tissue sarcoma sample - BO112-011-baseline
- GSM8581963 scRNA-seq of human soft tissue sarcoma sample - BO112-013-baseline
- GSM8581964 scRNA-seq of human soft tissue sarcoma sample - BO112-015-baseline
- GSM8581965 scRNA-seq of human soft tissue sarcoma sample - BO112-016-surgery
- GSM8581966 scRNA-seq of human soft tissue sarcoma sample - BO112-017-baseline
- GSE240287 RNA-sequencing of matched samples from rhabdomyosarcoma samples, obtained before therapy and mid-treatment resection 18 samples same disease briefing · shares rna-sequencing
- GSE312030 Combined inhibition of HRAS and MEK induces tumor regression and restores myogenic differentiation in HRAS-mutant rhabdomyosarcoma 159 samples same disease briefing
- GSE273829 GABA promotes resistance to immunotherapy of patients with TLS-positive tumors [RNA-seq] 92 samples same disease briefing
- GSE300974 CDK8 Inhibition Releases the Muscle Differentiation Blockade in Fusion-driven Alveolar Rhabdomyosarcoma [RNA-seq] 30 samples same disease briefing
- GSE314949 RNA Seq of rhabdomyosarcoma cells with sgRNA targeting oncofusion interacting proteins 30 samples same disease briefing
- GSE279954 mRNA/sRNA Co-Sequencing Reveals Multiple New Targeted Therapy Candidates in Rhabdomyosarcoma 26 samples same disease briefing
- GSE292872 FANCM is Required for the PAX3::FOXO1-Driven Oncogenic Program in Rhabdomyosarcoma [RNA-Seq] 21 samples same disease briefing
- GSE144190 Systematic profiling of synovial sarcoma transcriptome 20 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.