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Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [bulk RNA-seq]

ABSTRACT: Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [bulk RNA-seq]

PROVIDER: PRJNA895390 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22081641_1.fastq.gz	Fastqsanger.gz
	SRR22081641_2.fastq.gz	Fastqsanger.gz
	SRR22081642_1.fastq.gz	Fastqsanger.gz
	SRR22081642_2.fastq.gz	Fastqsanger.gz
	SRR22081643_1.fastq.gz	Fastqsanger.gz

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Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

| PRJNA981645 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

| PRJNA981646 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

| PRJNA895388 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state

Project description:Vestibular schwannomas (VS) are benign tumors that lead to significant neurologic and otologic morbidity. How VS heterogeneity and the tumor microenvironment (TME) contribute to the pathogenesis of these tumors remains poorly understood. We performed scRNA-seq on 15 VS samples, with paired scATAC-seq (n=6) and exome sequencing (n=12). We identified diverse Schwann cell (SC), stromal, and immune populations in the VS TME and found that repair-like and MHC-II antigen presenting subtype SCs are associated with increased myeloid cell infiltrate, implicating a nerve injury-like process. Deconvolution of RNA-expression data from 195 tumors revealed Injury-like tumors are associated with larger tumor size, and scATAC-seq identified transcription factors associated with nerve repair among SCs from Injury-like tumors. Ligand-receptor analysis and in vitro experiments suggested that SCs recruit monocytes. Our study indicates that Injury-like SCs may cause tumor growth via myeloid cell recruitment and identifies molecular pathways that may be targeted to prevent tumor progression. This SuperSeries is composed of the SubSeries listed below. Matching whole exome sequencing data is available via NCBI dbGaP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA981645/).

2023-09-15 | GSE216784 | GEO

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [scRNA-seq]

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [scRNA-seq]

| PRJNA895392 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [scATAC-seq]

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [scATAC-seq]

| PRJNA895391 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [scATAC-seq]

Project description:Vestibular schwannomas (VS) are benign tumors that lead to significant neurologic and otologic morbidity. How VS heterogeneity and the tumor microenvironment (TME) contribute to the pathogenesis of these tumors remains poorly understood. We performed scRNA-seq on 15 VS samples, with paired scATAC-seq (n=6) and exome sequencing (n=12). We identified diverse Schwann cell (SC), stromal, and immune populations in the VS TME and found that repair-like and MHC-II antigen presenting subtype SCs are associated with increased myeloid cell infiltrate, implicating a nerve injury-like process. Deconvolution of RNA-expression data from 195 tumors revealed Injury-like tumors are associated with larger tumor size, and scATAC-seq identified transcription factors associated with nerve repair among SCs from Injury-like tumors. Ligand-receptor analysis and in vitro experiments suggested that SCs recruit monocytes. Our study indicates that Injury-like SCs may cause tumor growth via myeloid cell recruitment and identifies molecular pathways that may be targeted to prevent tumor progression. This SubSeries is part of a SuperSeries (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216784). Matching whole exome sequencing data is available via NCBI dbGaP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA981645/).

2023-09-15 | GSE216782 | GEO

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [scRNA-seq]

Project description:Vestibular schwannomas (VS) are benign tumors that lead to significant neurologic and otologic morbidity. How VS heterogeneity and the tumor microenvironment (TME) contribute to the pathogenesis of these tumors remains poorly understood. We performed scRNA-seq on 15 VS samples, with paired scATAC-seq (n=6) and exome sequencing (n=12). We identified diverse Schwann cell (SC), stromal, and immune populations in the VS TME and found that repair-like and MHC-II antigen presenting subtype SCs are associated with increased myeloid cell infiltrate, implicating a nerve injury-like process. Deconvolution of RNA-expression data from 195 tumors revealed Injury-like tumors are associated with larger tumor size, and scATAC-seq identified transcription factors associated with nerve repair among SCs from Injury-like tumors. Ligand-receptor analysis and in vitro experiments suggested that SCs recruit monocytes. Our study indicates that Injury-like SCs may cause tumor growth via myeloid cell recruitment and identifies molecular pathways that may be targeted to prevent tumor progression. This SubSeries is part of a SuperSeries (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216784). Matching whole exome sequencing data is available via NCBI dbGaP (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA981645/).

2023-09-15 | GSE216783 | GEO

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [RNA-seq-invitro]

Project description:Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [RNA-seq-invitro]

| PRJNA992075 | ENA

Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state [RNA-seq-invitro]

Project description:Vestibular schwannomas (VS) are benign tumors that lead to significant neurologic and otologic morbidity. How VS heterogeneity and the tumor microenvironment (TME) contribute to the pathogenesis of these tumors remains poorly understood. We performed scRNA-seq on 15 VS samples, with paired scATAC-seq (n=6) and exome sequencing (n=12). We identified diverse Schwann cell (SC), stromal, and immune populations in the VS TME and found that repair-like and MHC-II antigen presenting subtype SCs are associated with increased myeloid cell infiltrate, implicating a nerve injury-like process. Deconvolution of RNA-expression data from 195 tumors revealed Injury-like tumors are associated with larger tumor size, and scATAC-seq identified transcription factors associated with nerve repair among SCs from Injury-like tumors. Ligand-receptor analysis and in vitro experiments suggested that SCs recruit monocytes. Our study indicates that Injury-like SCs may cause tumor growth via myeloid cell recruitment and identifies molecular pathways that may be targeted to prevent tumor progression. This SubSeries is part of a SuperSeries (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216784).

2023-09-15 | GSE236735 | GEO

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