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Illumina Inc 100 bp paired end mode
Changes in the proportion of cortical NSPC subtypes and neurons during human and chimpanzee cerebral organoid development. ( A ) Cryosections of cortical regions from human and chimpanzee organoids at day 28 and day 52 immunostained for PAX6 (magenta) and TBR2 (green) combined with DAPI staining. Scale bars; D28, 10 μm; D52, 20 μm. Insets in the D52 merge images show selected areas with PAX6+TBR2+ double-positive nuclei (arrowheads) at higher magnification. ( B ) Quantification of the percentage of PAX6+TBR2–, PAX6+TBR2+, PAX6–TBR2+ and PAX6–TBR2– cortical cells in human (light grey) and chimpanzee (dark grey) organoids at D28 (n = 5 organoids, 50 μm wide field) and D52-D54 (n = 17 organoids, <t>100</t> μm wide field). Error bars, SEM; *p
100 Bp Paired End Mode, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/100 bp paired end mode/product/Illumina Inc
Average 94 stars, based on 32 article reviews
Price from $9.99 to $1999.99
100 bp paired end mode - by Bioz Stars, 2020-05
94/100 stars

Images

1) Product Images from "Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development"

Article Title: Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

Journal: eLife

doi: 10.7554/eLife.18683

Changes in the proportion of cortical NSPC subtypes and neurons during human and chimpanzee cerebral organoid development. ( A ) Cryosections of cortical regions from human and chimpanzee organoids at day 28 and day 52 immunostained for PAX6 (magenta) and TBR2 (green) combined with DAPI staining. Scale bars; D28, 10 μm; D52, 20 μm. Insets in the D52 merge images show selected areas with PAX6+TBR2+ double-positive nuclei (arrowheads) at higher magnification. ( B ) Quantification of the percentage of PAX6+TBR2–, PAX6+TBR2+, PAX6–TBR2+ and PAX6–TBR2– cortical cells in human (light grey) and chimpanzee (dark grey) organoids at D28 (n = 5 organoids, 50 μm wide field) and D52-D54 (n = 17 organoids, 100 μm wide field). Error bars, SEM; *p
Figure Legend Snippet: Changes in the proportion of cortical NSPC subtypes and neurons during human and chimpanzee cerebral organoid development. ( A ) Cryosections of cortical regions from human and chimpanzee organoids at day 28 and day 52 immunostained for PAX6 (magenta) and TBR2 (green) combined with DAPI staining. Scale bars; D28, 10 μm; D52, 20 μm. Insets in the D52 merge images show selected areas with PAX6+TBR2+ double-positive nuclei (arrowheads) at higher magnification. ( B ) Quantification of the percentage of PAX6+TBR2–, PAX6+TBR2+, PAX6–TBR2+ and PAX6–TBR2– cortical cells in human (light grey) and chimpanzee (dark grey) organoids at D28 (n = 5 organoids, 50 μm wide field) and D52-D54 (n = 17 organoids, 100 μm wide field). Error bars, SEM; *p

Techniques Used: Staining

Cell cycle assignment for differential gene expression analysis. ( A ) Hierarchical clustering was used to identify human organoid APs that most strongly expressed genes enriched in G2M phase of the cell cycle (red). The genes were identified from PCA on fetal cortex progenitor cells (top 100 correlating genes) ( Camp et al., 2015 ). The cluster with weakest expression of these G2M associated genes was assigned as G1 phase (blue). Intermediate cells (grey) were discarded from differential gene expression analysis. ( B ) A previously published method was used to computationally assign cell-cycle stage based on a machine-learning approach ( Scialdone et al., 2015 ). This method was generally consistent with our assignment based on the hierarchical clustering presented in panel A . ( C – F ) The same approach was used to identify the chimpanzee organoid APs, endothelial cells (ECs), and iPSCs that most highly express G2M markers. Note that all iPSCs analyzed highly expressed most of the G2M marker genes. DOI: http://dx.doi.org/10.7554/eLife.18683.026
Figure Legend Snippet: Cell cycle assignment for differential gene expression analysis. ( A ) Hierarchical clustering was used to identify human organoid APs that most strongly expressed genes enriched in G2M phase of the cell cycle (red). The genes were identified from PCA on fetal cortex progenitor cells (top 100 correlating genes) ( Camp et al., 2015 ). The cluster with weakest expression of these G2M associated genes was assigned as G1 phase (blue). Intermediate cells (grey) were discarded from differential gene expression analysis. ( B ) A previously published method was used to computationally assign cell-cycle stage based on a machine-learning approach ( Scialdone et al., 2015 ). This method was generally consistent with our assignment based on the hierarchical clustering presented in panel A . ( C – F ) The same approach was used to identify the chimpanzee organoid APs, endothelial cells (ECs), and iPSCs that most highly express G2M markers. Note that all iPSCs analyzed highly expressed most of the G2M marker genes. DOI: http://dx.doi.org/10.7554/eLife.18683.026

Techniques Used: Expressing, Marker

2) Product Images from "Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer"

Article Title: Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

Journal: Nature Communications

doi: 10.1038/ncomms15081

Intratumoral heterogeneity in primary breast tumours. ( a ) Unsupervised PCA on the transcriptome, indicating a mixed distribution of intra- and interpatient cells. Individual cells are coloured yellow for luminal A, green for luminal B, blue for HER2, and red for TNBC tumours. This colour scheme is maintained throughout the manuscript. ( b ) Individual cells exhibiting gene expression heterogeneity for ER ( ESR1 ), PR ( PGR ) and HER2 ( ERBB2 ). The overall single-cell expression profiles agree with the bulk tumour expression profiles and the pathology results. ( c ) Haematoxylin and eosin staining on formalin-fixed paraffin-embedded slides. Microscopic findings indicated carcinoma and non-carcinoma cells, including tumour-infiltrating lymphocytes 9 (TIL, 1–60%). Most of the TNBC tumours except BC10 were heavily infiltrated with lymphocytes, whereas luminal A tumours showed enrichment with carcinoma cells. Scale bar, 100 μm. ( d ) A part of the tumour tissue in c is magnified to show non-neoplastic cellular components as a representative. Scale bar, 25 μm.
Figure Legend Snippet: Intratumoral heterogeneity in primary breast tumours. ( a ) Unsupervised PCA on the transcriptome, indicating a mixed distribution of intra- and interpatient cells. Individual cells are coloured yellow for luminal A, green for luminal B, blue for HER2, and red for TNBC tumours. This colour scheme is maintained throughout the manuscript. ( b ) Individual cells exhibiting gene expression heterogeneity for ER ( ESR1 ), PR ( PGR ) and HER2 ( ERBB2 ). The overall single-cell expression profiles agree with the bulk tumour expression profiles and the pathology results. ( c ) Haematoxylin and eosin staining on formalin-fixed paraffin-embedded slides. Microscopic findings indicated carcinoma and non-carcinoma cells, including tumour-infiltrating lymphocytes 9 (TIL, 1–60%). Most of the TNBC tumours except BC10 were heavily infiltrated with lymphocytes, whereas luminal A tumours showed enrichment with carcinoma cells. Scale bar, 100 μm. ( d ) A part of the tumour tissue in c is magnified to show non-neoplastic cellular components as a representative. Scale bar, 25 μm.

Techniques Used: Expressing, Staining, Formalin-fixed Paraffin-Embedded

3) Product Images from "Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers"

Article Title: Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers

Journal: Genome Biology

doi: 10.1186/s13059-019-1848-3

Predictive biomarkers for response to PARP inhibitors. a Volcano plot representation of gene-drug interactions in gynecologic tumors. b Waterfall plot enumerating individual tumor response to olaparib with BRCA1/2 and TP53 mutation status. c Receiver operating characteristic curve plotted for the sensitivity versus 100 - specificity values for predicting olaparib response rates using BRCA1/2 and TP53 mutation status. d Drug response assessment of olaparib on OVISE cell-line that has been stably transduced with/without TP53 - R249S , T273H , or R175H mutation. Dose response curves were generated using percent survival of cells under olaparib treatment for 4 days on 9 different doses from 200 to 0.78 μM. P values in a —two-sided Wilcoxon’s rank-sum test, and in c —two-sided binomial exact test
Figure Legend Snippet: Predictive biomarkers for response to PARP inhibitors. a Volcano plot representation of gene-drug interactions in gynecologic tumors. b Waterfall plot enumerating individual tumor response to olaparib with BRCA1/2 and TP53 mutation status. c Receiver operating characteristic curve plotted for the sensitivity versus 100 - specificity values for predicting olaparib response rates using BRCA1/2 and TP53 mutation status. d Drug response assessment of olaparib on OVISE cell-line that has been stably transduced with/without TP53 - R249S , T273H , or R175H mutation. Dose response curves were generated using percent survival of cells under olaparib treatment for 4 days on 9 different doses from 200 to 0.78 μM. P values in a —two-sided Wilcoxon’s rank-sum test, and in c —two-sided binomial exact test

Techniques Used: Mutagenesis, Stable Transfection, Transduction, Generated

4) Product Images from "SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells"

Article Title: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells

Journal: Genome Research

doi: 10.1101/gr.223263.117

Principles of the SIDR method. ( A ) Schematic of the SIDR method. (WGA) whole-genome amplification; (WTA) whole transcriptome amplification. ( B , C ) Immunostaining of the nucleus after cell lysis. Fluorescence images of MCF7 cells in isotonic ( B ) and hypotonic ( C ) conditions. The nuclear lamina, plasma membrane, and nucleus were stained by the Alexa 488-labeled anti-Lamin B2 antibody (green), CellMask (red), and DAPI (blue), respectively. ( D ) The effect of cell lysis on the recovery rate of cells. The recovery rate dramatically depended on whether anti-EPCAM antibody-conjugated microbeads were bound to cells before or after cell lysis as indicated at the bottom of the graph. Approximately 100 MCF7 cells underwent bead binding and/or cell lysis and were magnetically recovered, except for control cells that were not bound to microbeads. The plot shows the number of cells recovered ( n = 3). ( E ) The effect of bead binding on the solubilization of the EPCAM protein. The levels of EPCAM, beta actin, and Lamin B2 proteins in cell lysates not solubilized during cell lysis were measured by Western blot ( n = 3).
Figure Legend Snippet: Principles of the SIDR method. ( A ) Schematic of the SIDR method. (WGA) whole-genome amplification; (WTA) whole transcriptome amplification. ( B , C ) Immunostaining of the nucleus after cell lysis. Fluorescence images of MCF7 cells in isotonic ( B ) and hypotonic ( C ) conditions. The nuclear lamina, plasma membrane, and nucleus were stained by the Alexa 488-labeled anti-Lamin B2 antibody (green), CellMask (red), and DAPI (blue), respectively. ( D ) The effect of cell lysis on the recovery rate of cells. The recovery rate dramatically depended on whether anti-EPCAM antibody-conjugated microbeads were bound to cells before or after cell lysis as indicated at the bottom of the graph. Approximately 100 MCF7 cells underwent bead binding and/or cell lysis and were magnetically recovered, except for control cells that were not bound to microbeads. The plot shows the number of cells recovered ( n = 3). ( E ) The effect of bead binding on the solubilization of the EPCAM protein. The levels of EPCAM, beta actin, and Lamin B2 proteins in cell lysates not solubilized during cell lysis were measured by Western blot ( n = 3).

Techniques Used: Whole Genome Amplification, Amplification, Immunostaining, Lysis, Fluorescence, Staining, Labeling, Binding Assay, Western Blot

Related Articles

Sequencing:

Article Title: Circulating tumor DNA shows variable clonal response of breast cancer during neoadjuvant chemotherapy
Article Snippet: .. Flow cells were sequenced in 100-bp paired-end mode using HiSeq 2500 v3 Sequencing-by-Synthesis Kits (Illumina) and analyzed using RTA v.1.12.4.2 or later. .. Sequence data processing Using BWA-mem (v 0.7.5) [ ], all raw data were aligned to the hg19 human reference, creating BAM files.

Article Title: ARID1B alterations identify aggressive tumors in neuroblastoma
Article Snippet: .. After enriched exome libraries were multiplexed, the libraries were sequenced using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS kit on the Illumina HiSeq 2500 sequencing platform (Illumina Inc., San Diego, CA, USA). .. The DNA sequence data were aligned to the human genome reference (hg19) using the MEM algorithm in BWA 0.7.5 [ ].

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: .. Sequencing of the exome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. Whole transcriptome sequencing The library construction for whole transcriptome sequencing was performed using Truseq RNA sample preparation v2 kit (Illumina).

Article Title: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells
Article Snippet: .. Sequencing libraries for WES were created using the SureSelect XT Human All Exon V5 kit (Agilent Technologies) and subsequently analyzed by the HiSeq 2500 systems (Illumina) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. All DNA sequencing data were aligned to build version hg19 of the human genome using BWA-MEM (version 0.7.4) ( ) with default option parameters.

Article Title: Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens
Article Snippet: .. Sequencing of the transcriptome library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina). .. Exome-sequencing data analysis The sequencing reads were aligned to the UCSC hg19 reference genome (downloaded from http://genome.ucsc.edu ) using Burrows-Wheeler Aligner (BWA)[ ], version 0.6.2 with default settings.

Article Title: Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer
Article Snippet: .. Sequencing libraries were constructed for the HiSeq 2500 system (Illumina) and sequenced using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (PE-402-4001, Illumina). ..

Flow Cytometry:

Article Title: Circulating tumor DNA shows variable clonal response of breast cancer during neoadjuvant chemotherapy
Article Snippet: .. Flow cells were sequenced in 100-bp paired-end mode using HiSeq 2500 v3 Sequencing-by-Synthesis Kits (Illumina) and analyzed using RTA v.1.12.4.2 or later. .. Sequence data processing Using BWA-mem (v 0.7.5) [ ], all raw data were aligned to the hg19 human reference, creating BAM files.

Construct:

Article Title: Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer
Article Snippet: .. Sequencing libraries were constructed for the HiSeq 2500 system (Illumina) and sequenced using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (PE-402-4001, Illumina). ..

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    Illumina Inc 100 bp paired end mode
    Changes in the proportion of cortical NSPC subtypes and neurons during human and chimpanzee cerebral organoid development. ( A ) Cryosections of cortical regions from human and chimpanzee organoids at day 28 and day 52 immunostained for PAX6 (magenta) and TBR2 (green) combined with DAPI staining. Scale bars; D28, 10 μm; D52, 20 μm. Insets in the D52 merge images show selected areas with PAX6+TBR2+ double-positive nuclei (arrowheads) at higher magnification. ( B ) Quantification of the percentage of PAX6+TBR2–, PAX6+TBR2+, PAX6–TBR2+ and PAX6–TBR2– cortical cells in human (light grey) and chimpanzee (dark grey) organoids at D28 (n = 5 organoids, 50 μm wide field) and D52-D54 (n = 17 organoids, <t>100</t> μm wide field). Error bars, SEM; *p
    100 Bp Paired End Mode, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/100 bp paired end mode/product/Illumina Inc
    Average 94 stars, based on 32 article reviews
    Price from $9.99 to $1999.99
    100 bp paired end mode - by Bioz Stars, 2020-05
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    Changes in the proportion of cortical NSPC subtypes and neurons during human and chimpanzee cerebral organoid development. ( A ) Cryosections of cortical regions from human and chimpanzee organoids at day 28 and day 52 immunostained for PAX6 (magenta) and TBR2 (green) combined with DAPI staining. Scale bars; D28, 10 μm; D52, 20 μm. Insets in the D52 merge images show selected areas with PAX6+TBR2+ double-positive nuclei (arrowheads) at higher magnification. ( B ) Quantification of the percentage of PAX6+TBR2–, PAX6+TBR2+, PAX6–TBR2+ and PAX6–TBR2– cortical cells in human (light grey) and chimpanzee (dark grey) organoids at D28 (n = 5 organoids, 50 μm wide field) and D52-D54 (n = 17 organoids, 100 μm wide field). Error bars, SEM; *p

    Journal: eLife

    Article Title: Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

    doi: 10.7554/eLife.18683

    Figure Lengend Snippet: Changes in the proportion of cortical NSPC subtypes and neurons during human and chimpanzee cerebral organoid development. ( A ) Cryosections of cortical regions from human and chimpanzee organoids at day 28 and day 52 immunostained for PAX6 (magenta) and TBR2 (green) combined with DAPI staining. Scale bars; D28, 10 μm; D52, 20 μm. Insets in the D52 merge images show selected areas with PAX6+TBR2+ double-positive nuclei (arrowheads) at higher magnification. ( B ) Quantification of the percentage of PAX6+TBR2–, PAX6+TBR2+, PAX6–TBR2+ and PAX6–TBR2– cortical cells in human (light grey) and chimpanzee (dark grey) organoids at D28 (n = 5 organoids, 50 μm wide field) and D52-D54 (n = 17 organoids, 100 μm wide field). Error bars, SEM; *p

    Article Snippet: Up to 192 cells were pooled and sequenced in 100-bp paired-end mode on one lane of an Illumina HiSeq 2500 platform (rapid mode).

    Techniques: Staining

    Cell cycle assignment for differential gene expression analysis. ( A ) Hierarchical clustering was used to identify human organoid APs that most strongly expressed genes enriched in G2M phase of the cell cycle (red). The genes were identified from PCA on fetal cortex progenitor cells (top 100 correlating genes) ( Camp et al., 2015 ). The cluster with weakest expression of these G2M associated genes was assigned as G1 phase (blue). Intermediate cells (grey) were discarded from differential gene expression analysis. ( B ) A previously published method was used to computationally assign cell-cycle stage based on a machine-learning approach ( Scialdone et al., 2015 ). This method was generally consistent with our assignment based on the hierarchical clustering presented in panel A . ( C – F ) The same approach was used to identify the chimpanzee organoid APs, endothelial cells (ECs), and iPSCs that most highly express G2M markers. Note that all iPSCs analyzed highly expressed most of the G2M marker genes. DOI: http://dx.doi.org/10.7554/eLife.18683.026

    Journal: eLife

    Article Title: Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

    doi: 10.7554/eLife.18683

    Figure Lengend Snippet: Cell cycle assignment for differential gene expression analysis. ( A ) Hierarchical clustering was used to identify human organoid APs that most strongly expressed genes enriched in G2M phase of the cell cycle (red). The genes were identified from PCA on fetal cortex progenitor cells (top 100 correlating genes) ( Camp et al., 2015 ). The cluster with weakest expression of these G2M associated genes was assigned as G1 phase (blue). Intermediate cells (grey) were discarded from differential gene expression analysis. ( B ) A previously published method was used to computationally assign cell-cycle stage based on a machine-learning approach ( Scialdone et al., 2015 ). This method was generally consistent with our assignment based on the hierarchical clustering presented in panel A . ( C – F ) The same approach was used to identify the chimpanzee organoid APs, endothelial cells (ECs), and iPSCs that most highly express G2M markers. Note that all iPSCs analyzed highly expressed most of the G2M marker genes. DOI: http://dx.doi.org/10.7554/eLife.18683.026

    Article Snippet: Up to 192 cells were pooled and sequenced in 100-bp paired-end mode on one lane of an Illumina HiSeq 2500 platform (rapid mode).

    Techniques: Expressing, Marker

    Intratumoral heterogeneity in primary breast tumours. ( a ) Unsupervised PCA on the transcriptome, indicating a mixed distribution of intra- and interpatient cells. Individual cells are coloured yellow for luminal A, green for luminal B, blue for HER2, and red for TNBC tumours. This colour scheme is maintained throughout the manuscript. ( b ) Individual cells exhibiting gene expression heterogeneity for ER ( ESR1 ), PR ( PGR ) and HER2 ( ERBB2 ). The overall single-cell expression profiles agree with the bulk tumour expression profiles and the pathology results. ( c ) Haematoxylin and eosin staining on formalin-fixed paraffin-embedded slides. Microscopic findings indicated carcinoma and non-carcinoma cells, including tumour-infiltrating lymphocytes 9 (TIL, 1–60%). Most of the TNBC tumours except BC10 were heavily infiltrated with lymphocytes, whereas luminal A tumours showed enrichment with carcinoma cells. Scale bar, 100 μm. ( d ) A part of the tumour tissue in c is magnified to show non-neoplastic cellular components as a representative. Scale bar, 25 μm.

    Journal: Nature Communications

    Article Title: Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

    doi: 10.1038/ncomms15081

    Figure Lengend Snippet: Intratumoral heterogeneity in primary breast tumours. ( a ) Unsupervised PCA on the transcriptome, indicating a mixed distribution of intra- and interpatient cells. Individual cells are coloured yellow for luminal A, green for luminal B, blue for HER2, and red for TNBC tumours. This colour scheme is maintained throughout the manuscript. ( b ) Individual cells exhibiting gene expression heterogeneity for ER ( ESR1 ), PR ( PGR ) and HER2 ( ERBB2 ). The overall single-cell expression profiles agree with the bulk tumour expression profiles and the pathology results. ( c ) Haematoxylin and eosin staining on formalin-fixed paraffin-embedded slides. Microscopic findings indicated carcinoma and non-carcinoma cells, including tumour-infiltrating lymphocytes 9 (TIL, 1–60%). Most of the TNBC tumours except BC10 were heavily infiltrated with lymphocytes, whereas luminal A tumours showed enrichment with carcinoma cells. Scale bar, 100 μm. ( d ) A part of the tumour tissue in c is magnified to show non-neoplastic cellular components as a representative. Scale bar, 25 μm.

    Article Snippet: Sequencing libraries were constructed for the HiSeq 2500 system (Illumina) and sequenced using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (PE-402-4001, Illumina).

    Techniques: Expressing, Staining, Formalin-fixed Paraffin-Embedded

    Predictive biomarkers for response to PARP inhibitors. a Volcano plot representation of gene-drug interactions in gynecologic tumors. b Waterfall plot enumerating individual tumor response to olaparib with BRCA1/2 and TP53 mutation status. c Receiver operating characteristic curve plotted for the sensitivity versus 100 - specificity values for predicting olaparib response rates using BRCA1/2 and TP53 mutation status. d Drug response assessment of olaparib on OVISE cell-line that has been stably transduced with/without TP53 - R249S , T273H , or R175H mutation. Dose response curves were generated using percent survival of cells under olaparib treatment for 4 days on 9 different doses from 200 to 0.78 μM. P values in a —two-sided Wilcoxon’s rank-sum test, and in c —two-sided binomial exact test

    Journal: Genome Biology

    Article Title: Pharmacogenomic analysis of patient-derived tumor cells in gynecologic cancers

    doi: 10.1186/s13059-019-1848-3

    Figure Lengend Snippet: Predictive biomarkers for response to PARP inhibitors. a Volcano plot representation of gene-drug interactions in gynecologic tumors. b Waterfall plot enumerating individual tumor response to olaparib with BRCA1/2 and TP53 mutation status. c Receiver operating characteristic curve plotted for the sensitivity versus 100 - specificity values for predicting olaparib response rates using BRCA1/2 and TP53 mutation status. d Drug response assessment of olaparib on OVISE cell-line that has been stably transduced with/without TP53 - R249S , T273H , or R175H mutation. Dose response curves were generated using percent survival of cells under olaparib treatment for 4 days on 9 different doses from 200 to 0.78 μM. P values in a —two-sided Wilcoxon’s rank-sum test, and in c —two-sided binomial exact test

    Article Snippet: Sequencing was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit on a HiSeq 2500 sequencing platform (Illumina, San Diego, CA, USA).

    Techniques: Mutagenesis, Stable Transfection, Transduction, Generated

    Principles of the SIDR method. ( A ) Schematic of the SIDR method. (WGA) whole-genome amplification; (WTA) whole transcriptome amplification. ( B , C ) Immunostaining of the nucleus after cell lysis. Fluorescence images of MCF7 cells in isotonic ( B ) and hypotonic ( C ) conditions. The nuclear lamina, plasma membrane, and nucleus were stained by the Alexa 488-labeled anti-Lamin B2 antibody (green), CellMask (red), and DAPI (blue), respectively. ( D ) The effect of cell lysis on the recovery rate of cells. The recovery rate dramatically depended on whether anti-EPCAM antibody-conjugated microbeads were bound to cells before or after cell lysis as indicated at the bottom of the graph. Approximately 100 MCF7 cells underwent bead binding and/or cell lysis and were magnetically recovered, except for control cells that were not bound to microbeads. The plot shows the number of cells recovered ( n = 3). ( E ) The effect of bead binding on the solubilization of the EPCAM protein. The levels of EPCAM, beta actin, and Lamin B2 proteins in cell lysates not solubilized during cell lysis were measured by Western blot ( n = 3).

    Journal: Genome Research

    Article Title: SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells

    doi: 10.1101/gr.223263.117

    Figure Lengend Snippet: Principles of the SIDR method. ( A ) Schematic of the SIDR method. (WGA) whole-genome amplification; (WTA) whole transcriptome amplification. ( B , C ) Immunostaining of the nucleus after cell lysis. Fluorescence images of MCF7 cells in isotonic ( B ) and hypotonic ( C ) conditions. The nuclear lamina, plasma membrane, and nucleus were stained by the Alexa 488-labeled anti-Lamin B2 antibody (green), CellMask (red), and DAPI (blue), respectively. ( D ) The effect of cell lysis on the recovery rate of cells. The recovery rate dramatically depended on whether anti-EPCAM antibody-conjugated microbeads were bound to cells before or after cell lysis as indicated at the bottom of the graph. Approximately 100 MCF7 cells underwent bead binding and/or cell lysis and were magnetically recovered, except for control cells that were not bound to microbeads. The plot shows the number of cells recovered ( n = 3). ( E ) The effect of bead binding on the solubilization of the EPCAM protein. The levels of EPCAM, beta actin, and Lamin B2 proteins in cell lysates not solubilized during cell lysis were measured by Western blot ( n = 3).

    Article Snippet: Sequencing libraries for WES were created using the SureSelect XT Human All Exon V5 kit (Agilent Technologies) and subsequently analyzed by the HiSeq 2500 systems (Illumina) using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).

    Techniques: Whole Genome Amplification, Amplification, Immunostaining, Lysis, Fluorescence, Staining, Labeling, Binding Assay, Western Blot