Longitudinal biopsies of fusion-positive rhabdomyosarcoma orthotopic xenografts
RNA-seq (gene expression) · human · 16 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)
- Samples
- 16 samples: 6 × SHAGGY_6260 day vs 5 × SHAGGY_6259 day vs 5 × SHAGGY_6251 dayGroups 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
- Single cell transcriptomic profiling identifies tumor-acquired and therapy-resistant cell states in pediatric rhabdomyosarcomaNature communications · 2024
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 GSE240308_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 PRJNA1003123 and SRA study SRP453873. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 3 replicated groups read from 16 sample titles; they account for 16 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.
- GSM7695888 SHAGGY_6260 day 0 SHAGGY_6260 day
- GSM7695889 SHAGGY_6260 day 3 SHAGGY_6260 day
- GSM7695890 SHAGGY_6260 day 7 SHAGGY_6260 day
- GSM7695891 SHAGGY_6260 day 14 SHAGGY_6260 day
- GSM7695892 SHAGGY_6260 day 21 SHAGGY_6260 day
- GSM7695893 SHAGGY_6260 day 32 SHAGGY_6260 day
- GSM7695894 SHAGGY_6259 day 0 SHAGGY_6259 day
- GSM7695895 SHAGGY_6259 day 3 SHAGGY_6259 day
- GSM7695896 SHAGGY_6259 day 7 SHAGGY_6259 day
- GSM7695897 SHAGGY_6259 day 14 SHAGGY_6259 day
- GSM7695898 SHAGGY_6259 day 21 SHAGGY_6259 day
- GSM7695899 SHAGGY_6251 day 0 SHAGGY_6251 day
- GSM7695900 SHAGGY_6251 day 3 SHAGGY_6251 day
- GSM7695901 SHAGGY_6251 day 7 SHAGGY_6251 day
- GSM7695902 SHAGGY_6251 day 14 SHAGGY_6251 day
- GSM7695903 SHAGGY_6251 day 21 SHAGGY_6251 day
- GSE291966 An annotated biobank of triple negative breast cancer patient-derived xenografts featuring treatment-naïve and longitudinal samples throughout neoadjuvant chemotherapy 92 samples shares longitudinal, xenografts
- GSE319124 Next-GenerationPediatric Cancer Models: Patient-Matched Orthotopic Xenografts, 3D Organoids, 2D Cultures, and Cell Lines for Identification of Therapeutic Vulnerabilities in Pediatric Solid Tumors [scRNAseq] 59 samples shares orthotopic, xenografts
- GSE140261 Longitudinal measures of RNA expression and disease activity in FSHD muscle biopsies 35 samples shares longitudinal, biopsies
- GSE202614 TLE3 function in rhabdomyosarcoma tumor xenografts. 20 samples shares rhabdomyosarcoma, xenografts
- GSE332748 PAX3::FOXO1-Targeting PROTAC Induces Myogenic Differentiation of Fusion-Positive Rhabdomyosarcoma Cells 6 samples shares rhabdomyosarcoma, fusion-positive
- GSE279337 Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma 40 samples shares rhabdomyosarcoma, fusion-positive
- GSE279336 Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma [CUT&Run] 34 samples shares rhabdomyosarcoma, fusion-positive
- GSE285855 Fusion-positive rhabdomyosarcoma oncofusions share a common interactome 10 samples shares rhabdomyosarcoma, fusion-positive
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.