Deconvolution of bulk RNA-Seq using single cell RNA-Seq

In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

3 Datasets

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Samples
EGAD00001009688	In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.	-
EGAD00001015450	Our study utilizes two novel techniques, cyclical immunofluorescence imaging and single-cell spatial transcriptomics, to spatially map the tumor microenvironment of a large sample set of pediatric high-grade gliomas (pHGG). Using these methods, we have identified an abundant immunosuppressive myeloid cell population that has not been described in the context of pediatric high-grade gliomas. We validate our findings using an in vitro assay, spatial analysis on additional pHGG biopsies, independent spatial transcriptomic data, bulk RNA sequencing data of an expanded cohort of in-house patients, and publicly available bulk RNA sequencing data of an even larger cohort of pHGG patients.	1
EGAD00001015502	Key objective Are the prognostic transcriptomic G1/G2 gene expression signature, MYC overexpression, and MYC amplification replicable stratifying biomarkers for future clinical trials in high-grade osteosarcoma? Knowledge gathered In an unselected cohort, the G2 gene expression signature and MYC overexpression, but not MYC amplification, were independently associated with poor event-free and overall survival. Relevance Transcriptomic biomarkers may serve as stratifying factors that guide the management of patients with high-grade osteosarcoma. Current data underlines the importance of prospective validation of the G1/G2 signature and MYC overexpression in an international, multicenter, study.	1