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| Status |
Public on Apr 06, 2022 |
| Title |
A single-cell/nucleus atlas of pediatric rhabdomyosarcoma |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Rhabdomyosarcoma (RMS) is the most soft tissue sarcoma of childhood and histologically mimics developing skeletal muscle. To better understand RMS, we performed single-cell RNA-seq of one embryonal subtype RMS (ERMS) and one alveolar subtype RMS (ARMS). We expanded our observations by performing single-nucleus RNA-seq of 18 patient tumors (12 ERMS, 6 ARMS). All 18 of these tumors were used to generate orthotopic patient-derived xenografts, and we performed single-cell RNA-seq of all 18 O-PDXs to compare heterogeneity between the original tumor and the patient-derived model. 15 of the O-PDXs underwent lentiviral barcoding, and lineage could be tracked using a separate dial-out PCR step during the single-cell RNA-seq workflow. We performed single-cell RNA-seq of an ex vivo organoid, showing that we can preserve heterogeneity in this model. We expanded our study to the epigenetic level by using single-cell ATAC-sequencing of 7 O-PDXs. Finally, we longitudinally tracked shifts in heterogeneity in an O-PDX model treated with chemotherapy.
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| Overall design |
We performed single-cell RNA-seq from 2 patient RMS tumors, 18 O-PDXs, and 1 organoid. Additionally, we performed single-nucleus RNA-seq from 18 patient RMS tumors and single-cell ATAC-seq from 7 O-PDXs. We also provide dialout PCR data from 15 RMS O-PDX that were used for lentiviral barcode experiments to track clonal lineages within O-PDXs.
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| Contributor(s) |
Patel A, Dyer M |
| Citation(s) |
35483358 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| P30 CA021765 |
Cancer Center Support Grant (CCSG) |
ST. JUDE CHILDREN'S RESEARCH HOSPITAL |
CHARLES ROBERTS |
| R01 CA219686 |
Novel Therapeutic Approaches for the Treatment of Rhabdomyosarcoma |
ST. JUDE CHILDREN'S RESEARCH HOSPITAL |
Michael A Dyer |
| U01 CA263969 |
In Vivo Testing of Novel Drug Combinations for Pediatric Soft Tissue Sarcomas |
ST. JUDE CHILDREN'S RESEARCH HOSPITAL |
Michael A Dyer |
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| |
| Submission date |
May 13, 2021 |
| Last update date |
Jul 06, 2022 |
| Contact name |
Michael Dyer |
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Developmental Neurobiology
|
| Street address |
262 Danny Thomas Pl MS 324
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (64)
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| Relations |
| BioProject |
PRJNA729647 |
| SRA |
SRP319643 |
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