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Series GSE200529 Query DataSets for GSE200529
Status Public on Jul 21, 2023
Title Dissociation Protocols used for Sarcoma Tissues Bias the Transcriptome observed in Single-cell and Single-nucleus RNA sequencing.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary To determine whether sarcomas – tumors of mesenchymal origin – are subject to the same technical artifacts, we profiled patient-derived tumor explants (PDXs) propagated from three aggressive subtypes: osteosarcoma, Ewing sarcoma (ES), desmoplastic small round cell tumor (DSRCT). Given the rarity of these sarcoma subtypes, we explored whether single-nuclei RNA-seq from more widely available archival frozen specimens could accurately be identified by gene expression signatures linked to tissue phenotype or pathognomonic fusion proteins.
 
Overall design In this work, we studied sarcomas from varying tissue origins, including osteosarcoma (OS), Ewing’s sarcoma (ES), and desmoplastic small round cell tumor (DSRCT). We used different dissociation protocols: Miltenyi Tumor Dissociation Kit, cold-active protease derived from Bacillus licheniformis, and Nuclei EZ Prep. These three protocols are described herein as Warm, Cold, and Nuclei protocols. For the OS specimens, we used the same Nuclei protocol and a different Warm protocol optimized for OS. For DSRCT and ES specimens, we performed the additional Cold protocol, using the cold-active protease, as we had more specimens available. Each sarcoma subtype included three PDX specimens derived from different patients. In total, we analyzed 125,831 whole-cells and nuclei across the three sarcoma subtypes and three dissociation protocols.
 
Contributor(s) Truong DD, Gopalakrishnan V, Gordon N, Daw NC, Ludwig JA
Citation(s) 37254069, 38575753, 38775859
Submission date Apr 09, 2022
Last update date Jul 01, 2024
Contact name Danh Truong
E-mail(s) dtruong4@mdanderson.org
Organization name MD Anderson Cancer Center
Street address 1515 Holcombe Blvd
City Houston
ZIP/Postal code TX
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (26)
GSM6035489 DSRCT-1 Cold Dissociation
GSM6035490 DSRCT-1 Nuclei Isolation
GSM6035491 DSRCT-1 Warm Dissociation
Relations
BioProject PRJNA825075

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Supplementary file Size Download File type/resource
GSE200529_RAW.tar 2.7 Gb (http)(custom) TAR (of CSV, H5)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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