High-throughput tissue dissection and cell purification with digital cytometry
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ABSTRACT:
PROVIDER: PRJNA524853 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:High-throughput tissue dissection and cell purification with digital cytometry [Affymetrix]
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Project description:High-throughput tissue dissection and cell purification with digital cytometry [scRNA-Seq]
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Project description:High-throughput tissue dissection and cell purification with digital cytometry [healthy adults]
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Project description:Tissue composition is a major determinant of phenotypic variation and a key factor influencing disease outcomes. Although scRNA-Seq has emerged as a powerful technique for characterizing cellular heterogeneity, it is currently impractical for large sample cohorts and cannot be applied to fixed specimens collected as part of routine clinical care. To overcome these challenges, we extended Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) into a new platform for in silico cytometry. Our approach enables the simultaneous inference of cell type abundance and cell type-specific gene expression profiles (GEPs) from bulk tissue transcriptomes. The utility of this integrated framework, called CIBERSORTx, is demonstrated in multiple tumor types, including melanoma, where single cell reference profiles are used to dissect primary clinical specimens, revealing cell type-specific signatures of driver mutations and immunotherapy response. We anticipate that digital cytometry will augment single cell profiling efforts, enabling cost-effective, high throughput tissue characterization without the need for antibodies, disaggregation, or viable cells.
2019-05-06 | GSE127462 | GEO
Project description:Tissue composition is a major determinant of phenotypic variation and a key factor influencing disease outcomes. Although scRNA-Seq has emerged as a powerful technique for characterizing cellular heterogeneity, it is currently impractical for large sample cohorts and cannot be applied to fixed specimens collected as part of routine clinical care. To overcome these challenges, we extended Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) into a new platform for in silico cytometry. Our approach enables the simultaneous inference of cell type abundance and cell type-specific gene expression profiles (GEPs) from bulk tissue transcriptomes. The utility of this integrated framework, called CIBERSORTx, is demonstrated in multiple tumor types, including melanoma, where single cell reference profiles are used to dissect primary clinical specimens, revealing cell type-specific signatures of driver mutations and immunotherapy response. We anticipate that digital cytometry will augment single cell profiling efforts, enabling cost-effective, high throughput tissue characterization without the need for antibodies, disaggregation, or viable cells.
2019-05-06 | GSE127813 | GEO
Project description:Tissue composition is a major determinant of phenotypic variation and a key factor influencing disease outcomes. Although scRNA-Seq has emerged as a powerful technique for characterizing cellular heterogeneity, it is currently impractical for large sample cohorts and cannot be applied to fixed specimens collected as part of routine clinical care. To overcome these challenges, we extended Cell type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) into a new platform for in silico cytometry. Our approach enables the simultaneous inference of cell type abundance and cell type-specific gene expression profiles (GEPs) from bulk tissue transcriptomes. The utility of this integrated framework, called CIBERSORTx, is demonstrated in multiple tumor types, including melanoma, where single cell reference profiles are used to dissect primary clinical specimens, revealing cell type-specific signatures of driver mutations and immunotherapy response. We anticipate that digital cytometry will augment single cell profiling efforts, enabling cost-effective, high throughput tissue characterization without the need for antibodies, disaggregation, or viable cells.
2019-05-06 | GSE127471 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-05-06 | GSE127472 | GEO
Project description:We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined “High-Throughput (HT-) SuperSAGE”. SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index (barcode) sequences are employed to discriminate tags from different samples. Such barcodes permit to enable researchers to analyze digital tags from many transcriptomes of many samples in a single sequencing run by simply pooling the libraries. Here, we demonstrated that HT-SuperSAGE provided highly sensitive, reproducible and accurate digital gene expression data. By increasing throughput for analysis in HT-SuperSAGE, various applications were expected and several examples of its applications were introduced in the present study, including analyses of laser-microdissected cells, biological replicates or tag extraction using different anchoring enzymes.
2010-10-01 | GSE20682 | GEO
Project description:We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined “High-Throughput (HT-) SuperSAGE”. SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index (barcode) sequences are employed to discriminate tags from different samples. Such barcodes permit to enable researchers to analyze digital tags from many transcriptomes of many samples in a single sequencing run by simply pooling the libraries. Here, we demonstrated that HT-SuperSAGE provided highly sensitive, reproducible and accurate digital gene expression data. By increasing throughput for analysis in HT-SuperSAGE, various applications were expected and several examples of its applications were introduced in the present study, including analyses of laser-microdissected cells, biological replicates or tag extraction using different anchoring enzymes. 27 different tissue samples from three different life organisms were analyzed. About 2 samples, three different anchoring enzymes were employed.
2010-09-30 | E-GEOD-20682 | biostudies-arrayexpress
Project description:We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies.
2015-07-14 | PXD001872 | Pride