The Experts below are selected from a list of 66117 Experts worldwide ranked by ideXlab platform
Samuel G Rodriques - One of the best experts on this subject based on the ideXlab platform.
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hypr seq single cell quantification of chosen rnas via hybridization and sequencing of DNA Probes
Proceedings of the National Academy of Sciences of the United States of America, 2020Co-Authors: Jamie L Marshall, Benjamin R Doughty, Vidya Subramanian, Qingbo Wang, Linlin M Chen, Samuel G Rodriques, Philine GuckelbergerAbstract:Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of hundreds of chosen genes in single cells. HyPR-seq involves hybridizing DNA Probes to RNA, distributing cells into nanoliter droplets, amplifying the Probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome single-cell RNA-sequencing, making HyPR-seq a powerful method for targeted RNA profiling in single cells.
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hypr seq single cell quantification of chosen rnas via hybridization and sequencing of DNA Probes
bioRxiv, 2020Co-Authors: Jamie L Marshall, Benjamin R Doughty, Vidya Subramanian, Qingbo Wang, Linlin M Chen, Samuel G Rodriques, Kaite Zhang, Philine Guckelberger, Charles P Fulco, Joseph NasserAbstract:Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of up to 100 chosen genes in single cells. HyPR-seq involves hybridizing DNA Probes to RNA, distributing cells into nanoliter droplets, amplifying the Probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects non-polyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome scRNA-seq, making HyPR-seq a powerful method for targeted RNA profiling in single cells.
Jiro Takahara - One of the best experts on this subject based on the ideXlab platform.
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quantitative and sensitive northern blot hybridization using pcr generated DNA Probes labeled with digoxigenin by nick translation
BioTechniques, 1993Co-Authors: Makoto Sato, Koji Murao, Mutsuhiko Mizobuchi, Jiro TakaharaAbstract:Northern blot hydridization is one of the most convenient methods of detecting an mRNA. Nonradioactive Northern blotting using digoxigenin (DIG) is becoming widely applied because it is rapid and safe. Previous studies have indicated that DIG-labeled RNA Probes are suitable for Northern blot hybridization. Here, the application of PCR-generated double-stranded DNA Probes labeled with DIG by nick translation is described. DNA Probes were synthesized by PCR, then labeled with DIG by nick translation
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Quantitative and sensitive northern blot hybridization using PCR-generated DNA Probes labeled with digoxigenin by nick translation.
BioTechniques, 1993Co-Authors: Makoto Sato, Koji Murao, Mutsuhiko Mizobuchi, Jiro TakaharaAbstract:Northern blot hybridization is one of the most convenient methods of detecting an mRNA. Nonradioactive Northern blotting using digoxigenin (DIG) is becoming widely applied because it is rapid and safe. Previous studies have indicated that DIG-labeled RNA Probes are suitable for Northern blot hybridization. Here, the application of PCR-generated double-stranded DNA Probes labeled with DIG by nick translation is described. DNA Probes were synthesized by PCR, then labeled with DIG by nick translation. Northern blot hybridization was performed using the DIG-labeled DNA Probes, and the signals were detected by means of a chemiluminescent reaction. A low amount of DIG-dUTP in the labeling reaction resulted in excellent Northern blots with low background. Densitometric analysis of the blots showed that the mRNA concentrations could be determined by densitometric analysis. The sensitivity of the DIG-Northern system was comparable to Northern blotting using 32P and was sufficiently sensitive to detect low-abundance mRNA.
Philine Guckelberger - One of the best experts on this subject based on the ideXlab platform.
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hypr seq single cell quantification of chosen rnas via hybridization and sequencing of DNA Probes
Proceedings of the National Academy of Sciences of the United States of America, 2020Co-Authors: Jamie L Marshall, Benjamin R Doughty, Vidya Subramanian, Qingbo Wang, Linlin M Chen, Samuel G Rodriques, Philine GuckelbergerAbstract:Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of hundreds of chosen genes in single cells. HyPR-seq involves hybridizing DNA Probes to RNA, distributing cells into nanoliter droplets, amplifying the Probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome single-cell RNA-sequencing, making HyPR-seq a powerful method for targeted RNA profiling in single cells.
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hypr seq single cell quantification of chosen rnas via hybridization and sequencing of DNA Probes
bioRxiv, 2020Co-Authors: Jamie L Marshall, Benjamin R Doughty, Vidya Subramanian, Qingbo Wang, Linlin M Chen, Samuel G Rodriques, Kaite Zhang, Philine Guckelberger, Charles P Fulco, Joseph NasserAbstract:Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of up to 100 chosen genes in single cells. HyPR-seq involves hybridizing DNA Probes to RNA, distributing cells into nanoliter droplets, amplifying the Probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects non-polyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome scRNA-seq, making HyPR-seq a powerful method for targeted RNA profiling in single cells.
Qingbo Wang - One of the best experts on this subject based on the ideXlab platform.
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hypr seq single cell quantification of chosen rnas via hybridization and sequencing of DNA Probes
Proceedings of the National Academy of Sciences of the United States of America, 2020Co-Authors: Jamie L Marshall, Benjamin R Doughty, Vidya Subramanian, Qingbo Wang, Linlin M Chen, Samuel G Rodriques, Philine GuckelbergerAbstract:Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of hundreds of chosen genes in single cells. HyPR-seq involves hybridizing DNA Probes to RNA, distributing cells into nanoliter droplets, amplifying the Probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome single-cell RNA-sequencing, making HyPR-seq a powerful method for targeted RNA profiling in single cells.
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hypr seq single cell quantification of chosen rnas via hybridization and sequencing of DNA Probes
bioRxiv, 2020Co-Authors: Jamie L Marshall, Benjamin R Doughty, Vidya Subramanian, Qingbo Wang, Linlin M Chen, Samuel G Rodriques, Kaite Zhang, Philine Guckelberger, Charles P Fulco, Joseph NasserAbstract:Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of up to 100 chosen genes in single cells. HyPR-seq involves hybridizing DNA Probes to RNA, distributing cells into nanoliter droplets, amplifying the Probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects non-polyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome scRNA-seq, making HyPR-seq a powerful method for targeted RNA profiling in single cells.
Jamie L Marshall - One of the best experts on this subject based on the ideXlab platform.
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hypr seq single cell quantification of chosen rnas via hybridization and sequencing of DNA Probes
Proceedings of the National Academy of Sciences of the United States of America, 2020Co-Authors: Jamie L Marshall, Benjamin R Doughty, Vidya Subramanian, Qingbo Wang, Linlin M Chen, Samuel G Rodriques, Philine GuckelbergerAbstract:Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of hundreds of chosen genes in single cells. HyPR-seq involves hybridizing DNA Probes to RNA, distributing cells into nanoliter droplets, amplifying the Probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome single-cell RNA-sequencing, making HyPR-seq a powerful method for targeted RNA profiling in single cells.
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hypr seq single cell quantification of chosen rnas via hybridization and sequencing of DNA Probes
bioRxiv, 2020Co-Authors: Jamie L Marshall, Benjamin R Doughty, Vidya Subramanian, Qingbo Wang, Linlin M Chen, Samuel G Rodriques, Kaite Zhang, Philine Guckelberger, Charles P Fulco, Joseph NasserAbstract:Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of up to 100 chosen genes in single cells. HyPR-seq involves hybridizing DNA Probes to RNA, distributing cells into nanoliter droplets, amplifying the Probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects non-polyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome scRNA-seq, making HyPR-seq a powerful method for targeted RNA profiling in single cells.