Differential%20Gene%20Expression%20Kits Search Results


visium spatial gene expression reagent kits—tissue optimization user guide  (10X Genomics)
90
10X Genomics visium spatial gene expression reagent kits—tissue optimization user guide
a , The SMA workflow and quality control design—nonembedded, snap-frozen samples are sectioned and thaw-mounted onto noncharged, barcoded <t>Visium</t> Gene Expression arrays. Tissue sections are then sprayed with MALDI matrices and MSI is performed. This is followed by H&E staining and imaging with bright field microscopy. Finally, sections are processed for SRT. We also designed the following three types of control samples: (1) MSI—samples processed with standard MALDI-MSI protocol on ITO conductive slides; (2) VISIUM—samples processed with standard Visium protocol on all four capture areas of a Visium Gene Expression array and (3) V-iCTRL—samples processed with Visium protocol, but MALDI-MSI was performed on other capture areas of a Visium Gene Expression array. b , Pairwise gene-to-gene and molecule-to-molecule correlations across biological replicates. Samples are named with short identifiers that reflect the technical conditions under which the sample was analyzed: MSI, stand-alone MALDI-MSI; SMA, SMA protocol; VISIUM, stand-alone Visium. Additional acronyms indicate the matrix used in the SMA protocol (FMP-10, DHB and 9-AA), the sample (m1, m3 or m4) and the serial number of the tissue section (one to nine for each section placed on either ITO or Visium slides). c , UMAP of SMA ST spots colored by sections (left), MALDI matrices (middle) and clusters (right). d , Top three marker genes with highest average log 2 fold change for each spatial cluster across biological replicates. e , Spatial plot of mouse brain tissue sections (striatal level, 0.49 mm from bregma) that illustrates clusters of transcripts for samples sprayed with three different MALDI matrices (FMP-10, 9-AA and DHB) and one sample processed with the stand-alone Visium protocol.
Visium Spatial Gene Expression Reagent Kits—Tissue Optimization User Guide, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/visium spatial gene expression reagent kits—tissue optimization user guide/product/10X Genomics
Average 90 stars, based on 1 article reviews
visium spatial gene expression reagent kits—tissue optimization user guide - by Bioz Stars, 2026-02
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gene expression user guide 10x genomics-cg000239 rev a  (10X Genomics)
90
10X Genomics gene expression user guide 10x genomics-cg000239 rev a
a , The SMA workflow and quality control design—nonembedded, snap-frozen samples are sectioned and thaw-mounted onto noncharged, barcoded <t>Visium</t> Gene Expression arrays. Tissue sections are then sprayed with MALDI matrices and MSI is performed. This is followed by H&E staining and imaging with bright field microscopy. Finally, sections are processed for SRT. We also designed the following three types of control samples: (1) MSI—samples processed with standard MALDI-MSI protocol on ITO conductive slides; (2) VISIUM—samples processed with standard Visium protocol on all four capture areas of a Visium Gene Expression array and (3) V-iCTRL—samples processed with Visium protocol, but MALDI-MSI was performed on other capture areas of a Visium Gene Expression array. b , Pairwise gene-to-gene and molecule-to-molecule correlations across biological replicates. Samples are named with short identifiers that reflect the technical conditions under which the sample was analyzed: MSI, stand-alone MALDI-MSI; SMA, SMA protocol; VISIUM, stand-alone Visium. Additional acronyms indicate the matrix used in the SMA protocol (FMP-10, DHB and 9-AA), the sample (m1, m3 or m4) and the serial number of the tissue section (one to nine for each section placed on either ITO or Visium slides). c , UMAP of SMA ST spots colored by sections (left), MALDI matrices (middle) and clusters (right). d , Top three marker genes with highest average log 2 fold change for each spatial cluster across biological replicates. e , Spatial plot of mouse brain tissue sections (striatal level, 0.49 mm from bregma) that illustrates clusters of transcripts for samples sprayed with three different MALDI matrices (FMP-10, 9-AA and DHB) and one sample processed with the stand-alone Visium protocol.
Gene Expression User Guide 10x Genomics Cg000239 Rev A, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/gene expression user guide 10x genomics-cg000239 rev a/product/10X Genomics
Average 90 stars, based on 1 article reviews
gene expression user guide 10x genomics-cg000239 rev a - by Bioz Stars, 2026-02
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abcg2 and 18s taqman gene expression kits  (Fisher Scientific)
90
Fisher Scientific abcg2 and 18s taqman gene expression kits
a , The SMA workflow and quality control design—nonembedded, snap-frozen samples are sectioned and thaw-mounted onto noncharged, barcoded <t>Visium</t> Gene Expression arrays. Tissue sections are then sprayed with MALDI matrices and MSI is performed. This is followed by H&E staining and imaging with bright field microscopy. Finally, sections are processed for SRT. We also designed the following three types of control samples: (1) MSI—samples processed with standard MALDI-MSI protocol on ITO conductive slides; (2) VISIUM—samples processed with standard Visium protocol on all four capture areas of a Visium Gene Expression array and (3) V-iCTRL—samples processed with Visium protocol, but MALDI-MSI was performed on other capture areas of a Visium Gene Expression array. b , Pairwise gene-to-gene and molecule-to-molecule correlations across biological replicates. Samples are named with short identifiers that reflect the technical conditions under which the sample was analyzed: MSI, stand-alone MALDI-MSI; SMA, SMA protocol; VISIUM, stand-alone Visium. Additional acronyms indicate the matrix used in the SMA protocol (FMP-10, DHB and 9-AA), the sample (m1, m3 or m4) and the serial number of the tissue section (one to nine for each section placed on either ITO or Visium slides). c , UMAP of SMA ST spots colored by sections (left), MALDI matrices (middle) and clusters (right). d , Top three marker genes with highest average log 2 fold change for each spatial cluster across biological replicates. e , Spatial plot of mouse brain tissue sections (striatal level, 0.49 mm from bregma) that illustrates clusters of transcripts for samples sprayed with three different MALDI matrices (FMP-10, 9-AA and DHB) and one sample processed with the stand-alone Visium protocol.
Abcg2 And 18s Taqman Gene Expression Kits, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/abcg2 and 18s taqman gene expression kits/product/Fisher Scientific
Average 90 stars, based on 1 article reviews
abcg2 and 18s taqman gene expression kits - by Bioz Stars, 2026-02
90/100 stars
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visium gene expression kit  (Illumina Inc)
90
Illumina Inc visium gene expression kit
a , The SMA workflow and quality control design—nonembedded, snap-frozen samples are sectioned and thaw-mounted onto noncharged, barcoded <t>Visium</t> Gene Expression arrays. Tissue sections are then sprayed with MALDI matrices and MSI is performed. This is followed by H&E staining and imaging with bright field microscopy. Finally, sections are processed for SRT. We also designed the following three types of control samples: (1) MSI—samples processed with standard MALDI-MSI protocol on ITO conductive slides; (2) VISIUM—samples processed with standard Visium protocol on all four capture areas of a Visium Gene Expression array and (3) V-iCTRL—samples processed with Visium protocol, but MALDI-MSI was performed on other capture areas of a Visium Gene Expression array. b , Pairwise gene-to-gene and molecule-to-molecule correlations across biological replicates. Samples are named with short identifiers that reflect the technical conditions under which the sample was analyzed: MSI, stand-alone MALDI-MSI; SMA, SMA protocol; VISIUM, stand-alone Visium. Additional acronyms indicate the matrix used in the SMA protocol (FMP-10, DHB and 9-AA), the sample (m1, m3 or m4) and the serial number of the tissue section (one to nine for each section placed on either ITO or Visium slides). c , UMAP of SMA ST spots colored by sections (left), MALDI matrices (middle) and clusters (right). d , Top three marker genes with highest average log 2 fold change for each spatial cluster across biological replicates. e , Spatial plot of mouse brain tissue sections (striatal level, 0.49 mm from bregma) that illustrates clusters of transcripts for samples sprayed with three different MALDI matrices (FMP-10, 9-AA and DHB) and one sample processed with the stand-alone Visium protocol.
Visium Gene Expression Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/visium gene expression kit/product/Illumina Inc
Average 90 stars, based on 1 article reviews
visium gene expression kit - by Bioz Stars, 2026-02
90/100 stars
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qpcr primers and master mix from rt2 real-time gene expression assay kits  (SuperArray Bioscience Corporation)
90
SuperArray Bioscience Corporation qpcr primers and master mix from rt2 real-time gene expression assay kits
a , The SMA workflow and quality control design—nonembedded, snap-frozen samples are sectioned and thaw-mounted onto noncharged, barcoded <t>Visium</t> Gene Expression arrays. Tissue sections are then sprayed with MALDI matrices and MSI is performed. This is followed by H&E staining and imaging with bright field microscopy. Finally, sections are processed for SRT. We also designed the following three types of control samples: (1) MSI—samples processed with standard MALDI-MSI protocol on ITO conductive slides; (2) VISIUM—samples processed with standard Visium protocol on all four capture areas of a Visium Gene Expression array and (3) V-iCTRL—samples processed with Visium protocol, but MALDI-MSI was performed on other capture areas of a Visium Gene Expression array. b , Pairwise gene-to-gene and molecule-to-molecule correlations across biological replicates. Samples are named with short identifiers that reflect the technical conditions under which the sample was analyzed: MSI, stand-alone MALDI-MSI; SMA, SMA protocol; VISIUM, stand-alone Visium. Additional acronyms indicate the matrix used in the SMA protocol (FMP-10, DHB and 9-AA), the sample (m1, m3 or m4) and the serial number of the tissue section (one to nine for each section placed on either ITO or Visium slides). c , UMAP of SMA ST spots colored by sections (left), MALDI matrices (middle) and clusters (right). d , Top three marker genes with highest average log 2 fold change for each spatial cluster across biological replicates. e , Spatial plot of mouse brain tissue sections (striatal level, 0.49 mm from bregma) that illustrates clusters of transcripts for samples sprayed with three different MALDI matrices (FMP-10, 9-AA and DHB) and one sample processed with the stand-alone Visium protocol.
Qpcr Primers And Master Mix From Rt2 Real Time Gene Expression Assay Kits, supplied by SuperArray Bioscience Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/qpcr primers and master mix from rt2 real-time gene expression assay kits/product/SuperArray Bioscience Corporation
Average 90 stars, based on 1 article reviews
qpcr primers and master mix from rt2 real-time gene expression assay kits - by Bioz Stars, 2026-02
90/100 stars
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gene expressions kits rneasy mini kit  (Qiagen)
90
Qiagen gene expressions kits rneasy mini kit
a , The SMA workflow and quality control design—nonembedded, snap-frozen samples are sectioned and thaw-mounted onto noncharged, barcoded <t>Visium</t> Gene Expression arrays. Tissue sections are then sprayed with MALDI matrices and MSI is performed. This is followed by H&E staining and imaging with bright field microscopy. Finally, sections are processed for SRT. We also designed the following three types of control samples: (1) MSI—samples processed with standard MALDI-MSI protocol on ITO conductive slides; (2) VISIUM—samples processed with standard Visium protocol on all four capture areas of a Visium Gene Expression array and (3) V-iCTRL—samples processed with Visium protocol, but MALDI-MSI was performed on other capture areas of a Visium Gene Expression array. b , Pairwise gene-to-gene and molecule-to-molecule correlations across biological replicates. Samples are named with short identifiers that reflect the technical conditions under which the sample was analyzed: MSI, stand-alone MALDI-MSI; SMA, SMA protocol; VISIUM, stand-alone Visium. Additional acronyms indicate the matrix used in the SMA protocol (FMP-10, DHB and 9-AA), the sample (m1, m3 or m4) and the serial number of the tissue section (one to nine for each section placed on either ITO or Visium slides). c , UMAP of SMA ST spots colored by sections (left), MALDI matrices (middle) and clusters (right). d , Top three marker genes with highest average log 2 fold change for each spatial cluster across biological replicates. e , Spatial plot of mouse brain tissue sections (striatal level, 0.49 mm from bregma) that illustrates clusters of transcripts for samples sprayed with three different MALDI matrices (FMP-10, 9-AA and DHB) and one sample processed with the stand-alone Visium protocol.
Gene Expressions Kits Rneasy Mini Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/gene expressions kits rneasy mini kit/product/Qiagen
Average 90 stars, based on 1 article reviews
gene expressions kits rneasy mini kit - by Bioz Stars, 2026-02
90/100 stars
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visium cytassist spatial gene expression kits for ffpe, human transcriptome 11x11mm  (10X Genomics)
90
10X Genomics visium cytassist spatial gene expression kits for ffpe, human transcriptome 11x11mm
a , The SMA workflow and quality control design—nonembedded, snap-frozen samples are sectioned and thaw-mounted onto noncharged, barcoded <t>Visium</t> Gene Expression arrays. Tissue sections are then sprayed with MALDI matrices and MSI is performed. This is followed by H&E staining and imaging with bright field microscopy. Finally, sections are processed for SRT. We also designed the following three types of control samples: (1) MSI—samples processed with standard MALDI-MSI protocol on ITO conductive slides; (2) VISIUM—samples processed with standard Visium protocol on all four capture areas of a Visium Gene Expression array and (3) V-iCTRL—samples processed with Visium protocol, but MALDI-MSI was performed on other capture areas of a Visium Gene Expression array. b , Pairwise gene-to-gene and molecule-to-molecule correlations across biological replicates. Samples are named with short identifiers that reflect the technical conditions under which the sample was analyzed: MSI, stand-alone MALDI-MSI; SMA, SMA protocol; VISIUM, stand-alone Visium. Additional acronyms indicate the matrix used in the SMA protocol (FMP-10, DHB and 9-AA), the sample (m1, m3 or m4) and the serial number of the tissue section (one to nine for each section placed on either ITO or Visium slides). c , UMAP of SMA ST spots colored by sections (left), MALDI matrices (middle) and clusters (right). d , Top three marker genes with highest average log 2 fold change for each spatial cluster across biological replicates. e , Spatial plot of mouse brain tissue sections (striatal level, 0.49 mm from bregma) that illustrates clusters of transcripts for samples sprayed with three different MALDI matrices (FMP-10, 9-AA and DHB) and one sample processed with the stand-alone Visium protocol.
Visium Cytassist Spatial Gene Expression Kits For Ffpe, Human Transcriptome 11x11mm, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/visium cytassist spatial gene expression kits for ffpe, human transcriptome 11x11mm/product/10X Genomics
Average 90 stars, based on 1 article reviews
visium cytassist spatial gene expression kits for ffpe, human transcriptome 11x11mm - by Bioz Stars, 2026-02
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chromium multiome atac+gene expression kits  (10X Genomics)
90
10X Genomics chromium multiome atac+gene expression kits
A: Overview of study design, data modalities, and analysis strategies. Single-cell and nucleus RNA-seq (Bayraktar S. et al. ), <t>Multiome,</t> and Visium spatial transcriptomics data were generated from a total of 23 human fetal hearts between the ages of 4 and 20 PCW. Euploid datasets and models were integrated with and mapped to the newly generated Trisomy 21 datasets (13 and 14 PCW). B: UMAP embedding of chromatin accessibility data of 63 cell types of the developing human heart and the great vessels, spread across 14 mid- and 6 coarse-grains. UMAP embedding of the cells based on the chromatin accessibility profile shares similar segregation patterns with the gene expression profile. C-D: Entropy score (Methods) of neighbourhoods of atrial or ventricular cardiomyocytes or myeloid cells. The UMAP embeddings (C) show neighbourhoods (Milo) identified using gene expression data and scVI latent space. The dot size shows the neighbourhood size and the colour shows the entropy score. The box plots (D) indicate the entropy scores of the neighbourhoods in each assigned cell type label. Data points represent neighbourhoods. p -values are provided for the comparison among groups of cell types as indicated (two-sided Kruskal-Wallis test, for multiple comparisons, post hoc analysis with Dunn’s test was performed with adjusting p-values using the Bonferroni method). E: UMAP embedding of estimated cell type abundances (cell2location) of the Visium spots across 22 spatial sections. Spots were annotated based on clustering, estimated abundance of cell types in each cluster, and histological structure as defined by expert annotations using H&E images (Methods). F: Representative Visium sections, which capture the whole heart, with structural annotations. G: Dotplot displaying the estimated fine-grained cell (columns) abundance per tissue structure annotation (rows). Summarised abundances were normalised for each cell type. AV: atrioventricular, AVN: AV node, GV: great vessel, H&E: hematoxylin and eosin, VCS: ventricular conduction system, VCSp: VCS proximal, CCF: common coordinate framework, GRN: gene regulatory network, PCW: post-conception weeks.
Chromium Multiome Atac+Gene Expression Kits, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/chromium multiome atac+gene expression kits/product/10X Genomics
Average 90 stars, based on 1 article reviews
chromium multiome atac+gene expression kits - by Bioz Stars, 2026-02
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gene expression assay kits human cox-2  (M.J Research Inc)
90
M.J Research Inc gene expression assay kits human cox-2
A: Overview of study design, data modalities, and analysis strategies. Single-cell and nucleus RNA-seq (Bayraktar S. et al. ), <t>Multiome,</t> and Visium spatial transcriptomics data were generated from a total of 23 human fetal hearts between the ages of 4 and 20 PCW. Euploid datasets and models were integrated with and mapped to the newly generated Trisomy 21 datasets (13 and 14 PCW). B: UMAP embedding of chromatin accessibility data of 63 cell types of the developing human heart and the great vessels, spread across 14 mid- and 6 coarse-grains. UMAP embedding of the cells based on the chromatin accessibility profile shares similar segregation patterns with the gene expression profile. C-D: Entropy score (Methods) of neighbourhoods of atrial or ventricular cardiomyocytes or myeloid cells. The UMAP embeddings (C) show neighbourhoods (Milo) identified using gene expression data and scVI latent space. The dot size shows the neighbourhood size and the colour shows the entropy score. The box plots (D) indicate the entropy scores of the neighbourhoods in each assigned cell type label. Data points represent neighbourhoods. p -values are provided for the comparison among groups of cell types as indicated (two-sided Kruskal-Wallis test, for multiple comparisons, post hoc analysis with Dunn’s test was performed with adjusting p-values using the Bonferroni method). E: UMAP embedding of estimated cell type abundances (cell2location) of the Visium spots across 22 spatial sections. Spots were annotated based on clustering, estimated abundance of cell types in each cluster, and histological structure as defined by expert annotations using H&E images (Methods). F: Representative Visium sections, which capture the whole heart, with structural annotations. G: Dotplot displaying the estimated fine-grained cell (columns) abundance per tissue structure annotation (rows). Summarised abundances were normalised for each cell type. AV: atrioventricular, AVN: AV node, GV: great vessel, H&E: hematoxylin and eosin, VCS: ventricular conduction system, VCSp: VCS proximal, CCF: common coordinate framework, GRN: gene regulatory network, PCW: post-conception weeks.
Gene Expression Assay Kits Human Cox 2, supplied by M.J Research Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/gene expression assay kits human cox-2/product/M.J Research Inc
Average 90 stars, based on 1 article reviews
gene expression assay kits human cox-2 - by Bioz Stars, 2026-02
90/100 stars
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single-cell multi-ome kits for epigenetic and gene expression profiling  (10X Genomics)
90
10X Genomics single-cell multi-ome kits for epigenetic and gene expression profiling
A: Overview of study design, data modalities, and analysis strategies. Single-cell and nucleus RNA-seq (Bayraktar S. et al. ), <t>Multiome,</t> and Visium spatial transcriptomics data were generated from a total of 23 human fetal hearts between the ages of 4 and 20 PCW. Euploid datasets and models were integrated with and mapped to the newly generated Trisomy 21 datasets (13 and 14 PCW). B: UMAP embedding of chromatin accessibility data of 63 cell types of the developing human heart and the great vessels, spread across 14 mid- and 6 coarse-grains. UMAP embedding of the cells based on the chromatin accessibility profile shares similar segregation patterns with the gene expression profile. C-D: Entropy score (Methods) of neighbourhoods of atrial or ventricular cardiomyocytes or myeloid cells. The UMAP embeddings (C) show neighbourhoods (Milo) identified using gene expression data and scVI latent space. The dot size shows the neighbourhood size and the colour shows the entropy score. The box plots (D) indicate the entropy scores of the neighbourhoods in each assigned cell type label. Data points represent neighbourhoods. p -values are provided for the comparison among groups of cell types as indicated (two-sided Kruskal-Wallis test, for multiple comparisons, post hoc analysis with Dunn’s test was performed with adjusting p-values using the Bonferroni method). E: UMAP embedding of estimated cell type abundances (cell2location) of the Visium spots across 22 spatial sections. Spots were annotated based on clustering, estimated abundance of cell types in each cluster, and histological structure as defined by expert annotations using H&E images (Methods). F: Representative Visium sections, which capture the whole heart, with structural annotations. G: Dotplot displaying the estimated fine-grained cell (columns) abundance per tissue structure annotation (rows). Summarised abundances were normalised for each cell type. AV: atrioventricular, AVN: AV node, GV: great vessel, H&E: hematoxylin and eosin, VCS: ventricular conduction system, VCSp: VCS proximal, CCF: common coordinate framework, GRN: gene regulatory network, PCW: post-conception weeks.
Single Cell Multi Ome Kits For Epigenetic And Gene Expression Profiling, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/single-cell multi-ome kits for epigenetic and gene expression profiling/product/10X Genomics
Average 90 stars, based on 1 article reviews
single-cell multi-ome kits for epigenetic and gene expression profiling - by Bioz Stars, 2026-02
90/100 stars
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sample preparation kits for illumina gene expression  (Illumina Inc)
90
Illumina Inc sample preparation kits for illumina gene expression
A: Overview of study design, data modalities, and analysis strategies. Single-cell and nucleus RNA-seq (Bayraktar S. et al. ), <t>Multiome,</t> and Visium spatial transcriptomics data were generated from a total of 23 human fetal hearts between the ages of 4 and 20 PCW. Euploid datasets and models were integrated with and mapped to the newly generated Trisomy 21 datasets (13 and 14 PCW). B: UMAP embedding of chromatin accessibility data of 63 cell types of the developing human heart and the great vessels, spread across 14 mid- and 6 coarse-grains. UMAP embedding of the cells based on the chromatin accessibility profile shares similar segregation patterns with the gene expression profile. C-D: Entropy score (Methods) of neighbourhoods of atrial or ventricular cardiomyocytes or myeloid cells. The UMAP embeddings (C) show neighbourhoods (Milo) identified using gene expression data and scVI latent space. The dot size shows the neighbourhood size and the colour shows the entropy score. The box plots (D) indicate the entropy scores of the neighbourhoods in each assigned cell type label. Data points represent neighbourhoods. p -values are provided for the comparison among groups of cell types as indicated (two-sided Kruskal-Wallis test, for multiple comparisons, post hoc analysis with Dunn’s test was performed with adjusting p-values using the Bonferroni method). E: UMAP embedding of estimated cell type abundances (cell2location) of the Visium spots across 22 spatial sections. Spots were annotated based on clustering, estimated abundance of cell types in each cluster, and histological structure as defined by expert annotations using H&E images (Methods). F: Representative Visium sections, which capture the whole heart, with structural annotations. G: Dotplot displaying the estimated fine-grained cell (columns) abundance per tissue structure annotation (rows). Summarised abundances were normalised for each cell type. AV: atrioventricular, AVN: AV node, GV: great vessel, H&E: hematoxylin and eosin, VCS: ventricular conduction system, VCSp: VCS proximal, CCF: common coordinate framework, GRN: gene regulatory network, PCW: post-conception weeks.
Sample Preparation Kits For Illumina Gene Expression, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/sample preparation kits for illumina gene expression/product/Illumina Inc
Average 90 stars, based on 1 article reviews
sample preparation kits for illumina gene expression - by Bioz Stars, 2026-02
90/100 stars
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rt2 real time gene expression assay kits qph00488a  (SuperArray Bioscience Corporation)
90
SuperArray Bioscience Corporation rt2 real time gene expression assay kits qph00488a
A: Overview of study design, data modalities, and analysis strategies. Single-cell and nucleus RNA-seq (Bayraktar S. et al. ), <t>Multiome,</t> and Visium spatial transcriptomics data were generated from a total of 23 human fetal hearts between the ages of 4 and 20 PCW. Euploid datasets and models were integrated with and mapped to the newly generated Trisomy 21 datasets (13 and 14 PCW). B: UMAP embedding of chromatin accessibility data of 63 cell types of the developing human heart and the great vessels, spread across 14 mid- and 6 coarse-grains. UMAP embedding of the cells based on the chromatin accessibility profile shares similar segregation patterns with the gene expression profile. C-D: Entropy score (Methods) of neighbourhoods of atrial or ventricular cardiomyocytes or myeloid cells. The UMAP embeddings (C) show neighbourhoods (Milo) identified using gene expression data and scVI latent space. The dot size shows the neighbourhood size and the colour shows the entropy score. The box plots (D) indicate the entropy scores of the neighbourhoods in each assigned cell type label. Data points represent neighbourhoods. p -values are provided for the comparison among groups of cell types as indicated (two-sided Kruskal-Wallis test, for multiple comparisons, post hoc analysis with Dunn’s test was performed with adjusting p-values using the Bonferroni method). E: UMAP embedding of estimated cell type abundances (cell2location) of the Visium spots across 22 spatial sections. Spots were annotated based on clustering, estimated abundance of cell types in each cluster, and histological structure as defined by expert annotations using H&E images (Methods). F: Representative Visium sections, which capture the whole heart, with structural annotations. G: Dotplot displaying the estimated fine-grained cell (columns) abundance per tissue structure annotation (rows). Summarised abundances were normalised for each cell type. AV: atrioventricular, AVN: AV node, GV: great vessel, H&E: hematoxylin and eosin, VCS: ventricular conduction system, VCSp: VCS proximal, CCF: common coordinate framework, GRN: gene regulatory network, PCW: post-conception weeks.
Rt2 Real Time Gene Expression Assay Kits Qph00488a, supplied by SuperArray Bioscience Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/rt2 real time gene expression assay kits qph00488a/product/SuperArray Bioscience Corporation
Average 90 stars, based on 1 article reviews
rt2 real time gene expression assay kits qph00488a - by Bioz Stars, 2026-02
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Image Search Results


a , The SMA workflow and quality control design—nonembedded, snap-frozen samples are sectioned and thaw-mounted onto noncharged, barcoded Visium Gene Expression arrays. Tissue sections are then sprayed with MALDI matrices and MSI is performed. This is followed by H&E staining and imaging with bright field microscopy. Finally, sections are processed for SRT. We also designed the following three types of control samples: (1) MSI—samples processed with standard MALDI-MSI protocol on ITO conductive slides; (2) VISIUM—samples processed with standard Visium protocol on all four capture areas of a Visium Gene Expression array and (3) V-iCTRL—samples processed with Visium protocol, but MALDI-MSI was performed on other capture areas of a Visium Gene Expression array. b , Pairwise gene-to-gene and molecule-to-molecule correlations across biological replicates. Samples are named with short identifiers that reflect the technical conditions under which the sample was analyzed: MSI, stand-alone MALDI-MSI; SMA, SMA protocol; VISIUM, stand-alone Visium. Additional acronyms indicate the matrix used in the SMA protocol (FMP-10, DHB and 9-AA), the sample (m1, m3 or m4) and the serial number of the tissue section (one to nine for each section placed on either ITO or Visium slides). c , UMAP of SMA ST spots colored by sections (left), MALDI matrices (middle) and clusters (right). d , Top three marker genes with highest average log 2 fold change for each spatial cluster across biological replicates. e , Spatial plot of mouse brain tissue sections (striatal level, 0.49 mm from bregma) that illustrates clusters of transcripts for samples sprayed with three different MALDI matrices (FMP-10, 9-AA and DHB) and one sample processed with the stand-alone Visium protocol.

Journal: Nature Biotechnology

Article Title: Spatial multimodal analysis of transcriptomes and metabolomes in tissues

doi: 10.1038/s41587-023-01937-y

Figure Lengend Snippet: a , The SMA workflow and quality control design—nonembedded, snap-frozen samples are sectioned and thaw-mounted onto noncharged, barcoded Visium Gene Expression arrays. Tissue sections are then sprayed with MALDI matrices and MSI is performed. This is followed by H&E staining and imaging with bright field microscopy. Finally, sections are processed for SRT. We also designed the following three types of control samples: (1) MSI—samples processed with standard MALDI-MSI protocol on ITO conductive slides; (2) VISIUM—samples processed with standard Visium protocol on all four capture areas of a Visium Gene Expression array and (3) V-iCTRL—samples processed with Visium protocol, but MALDI-MSI was performed on other capture areas of a Visium Gene Expression array. b , Pairwise gene-to-gene and molecule-to-molecule correlations across biological replicates. Samples are named with short identifiers that reflect the technical conditions under which the sample was analyzed: MSI, stand-alone MALDI-MSI; SMA, SMA protocol; VISIUM, stand-alone Visium. Additional acronyms indicate the matrix used in the SMA protocol (FMP-10, DHB and 9-AA), the sample (m1, m3 or m4) and the serial number of the tissue section (one to nine for each section placed on either ITO or Visium slides). c , UMAP of SMA ST spots colored by sections (left), MALDI matrices (middle) and clusters (right). d , Top three marker genes with highest average log 2 fold change for each spatial cluster across biological replicates. e , Spatial plot of mouse brain tissue sections (striatal level, 0.49 mm from bregma) that illustrates clusters of transcripts for samples sprayed with three different MALDI matrices (FMP-10, 9-AA and DHB) and one sample processed with the stand-alone Visium protocol.

Article Snippet: Visium Spatial Gene Expression and Tissue Optimization slides, with the exception of the human postmortem sample, were processed according to the corresponding latest versions of the 10X Genomics protocols (Visium Spatial Gene Expression Reagent Kits—Tissue Optimization User Guide, document CG000238 Rev E, 10X Genomics, (February 2022); Visium Spatial Gene Expression Reagent Kits—User Guide, document CG000239 Rev F, 10X Genomics, (January 2022) and Methanol Fixation, H&E Staining and Imaging for Visium Spatial Protocols, document CG000160 Rev C, 10X Genomics), without any modification.

Techniques: Control, Gene Expression, Staining, Imaging, Microscopy, Marker

(a) Eight mouse brain tissue sections from the striatal level of the same animal (n = 8) were mounted onto a Visium Tissue Optimization slide and sprayed with four different MALDI matrices (DHB, norharmane (analyzed in both positive and negative mode, shown as Nor+ and Nor-), 9-AA and FMP-10). Areas delimited by red lines: regions of interest imaged with MALDI-MSI. Scalebars: 1 mm. (b) Representative MSI results from: i) m/z 426.36, C18:1 L-Carnitine (DHB); ii) m/z 857.52, PI(36:4) (Nor-); iii) m/z 788.62 PC(36:1) (Nor+); iv,v) m/z 303.24, arachidonic acid (9-AA); vi) m/z 371.17, GABA (FMP-10). Nor+ and Nor-: Norharmane analyzed in positive and negative mode, respectively. Scalebars: 1 mm, except iv and v where it is 2 mm. (c) Fluorescence microscopy images of mRNA footprint captured with polydT probes after MALDI-MSI. Colored lines (i, iv, vi, viii, x, xii) demarcate areas imaged with MALDI-MSI, while gray lines (ii, iii, v, vii, ix, xi, xiii, xiv) demarcate areas not imaged with MALDI-MSI and used as controls. Scalebars: 1 mm. (d) Fluorescence intensity of tissue areas imaged or not with MALDI-MSI. The upper and lower limit of the box represent the +1 and −1 standard deviation from the mean, the horizontal line inside the box represents the mean fluorescence intensity, and the upper and lower limits of the whiskers represent the maximum and minimum fluorescence intensity values. The results shown in panels (A-C) belong to eight consecutive tissue sections from n = 1 biologically independent sample examined over one independent experiment (all the sections were placed on one Visium Tissue Optimization array). The areas in square pixels over which the statistics is derived are the following: i = 768047, ii=355349, iii=843707, iv=866085, v = 578711, vi=805789, vii=562179, viii=846042, ix=317398, x = 843416, xi=611982, xii=779667, xiii=727089, xiv=751797. (e) A mouse brain tissue sections (n = 1) from the hippocampus level was mounted onto an ITO slide and sprayed FMP-10. The area delimited by a red line demarcates the region of interest imaged with MALDI-MSI. (f) Targeted In Situ Sequencing data demonstrate similar rolling circle product (RCP) density generated from MALDI-MSI processed region (upper right panel) and non-processed region (lower right panel) for demarcated regions of interest in the mouse coronal section (n = 1). Targeted ISS simultaneously probed for housekeeping gene, Gapdh labeled in Magenta (Cy5), and a panel of five control genes - Foxj1, Plp1, Lamp5, Rorb and Kcnip2 that are labeled in Cyan (AF750). (g) Mean Cy5 and AF750 fluorescence intensity of rolling circle products in tissue areas imaged or not with MALDI-MSI.The results shown in panels (E-G) belong to one tissue section from n = 1 biologically independent sample examined over one independent experiment. The number of RCPs detected in the MALDI-MSI processed region in AF750 and Cy5 and the number of RCPs detected in the non-processed region in AF750 and Cy5 respectively, which the statistics is derived from, are the following: n = 3830,n = 18231, n = 3051,n = 18193. The lower and upper hinges of the boxplot correspond to the first and third quartiles (the 25th and 75th percentiles), the central white dot corresponds to the median, the upper and lower whiskers extend from the hinge to the maximum or minimum respectively.

Journal: Nature Biotechnology

Article Title: Spatial multimodal analysis of transcriptomes and metabolomes in tissues

doi: 10.1038/s41587-023-01937-y

Figure Lengend Snippet: (a) Eight mouse brain tissue sections from the striatal level of the same animal (n = 8) were mounted onto a Visium Tissue Optimization slide and sprayed with four different MALDI matrices (DHB, norharmane (analyzed in both positive and negative mode, shown as Nor+ and Nor-), 9-AA and FMP-10). Areas delimited by red lines: regions of interest imaged with MALDI-MSI. Scalebars: 1 mm. (b) Representative MSI results from: i) m/z 426.36, C18:1 L-Carnitine (DHB); ii) m/z 857.52, PI(36:4) (Nor-); iii) m/z 788.62 PC(36:1) (Nor+); iv,v) m/z 303.24, arachidonic acid (9-AA); vi) m/z 371.17, GABA (FMP-10). Nor+ and Nor-: Norharmane analyzed in positive and negative mode, respectively. Scalebars: 1 mm, except iv and v where it is 2 mm. (c) Fluorescence microscopy images of mRNA footprint captured with polydT probes after MALDI-MSI. Colored lines (i, iv, vi, viii, x, xii) demarcate areas imaged with MALDI-MSI, while gray lines (ii, iii, v, vii, ix, xi, xiii, xiv) demarcate areas not imaged with MALDI-MSI and used as controls. Scalebars: 1 mm. (d) Fluorescence intensity of tissue areas imaged or not with MALDI-MSI. The upper and lower limit of the box represent the +1 and −1 standard deviation from the mean, the horizontal line inside the box represents the mean fluorescence intensity, and the upper and lower limits of the whiskers represent the maximum and minimum fluorescence intensity values. The results shown in panels (A-C) belong to eight consecutive tissue sections from n = 1 biologically independent sample examined over one independent experiment (all the sections were placed on one Visium Tissue Optimization array). The areas in square pixels over which the statistics is derived are the following: i = 768047, ii=355349, iii=843707, iv=866085, v = 578711, vi=805789, vii=562179, viii=846042, ix=317398, x = 843416, xi=611982, xii=779667, xiii=727089, xiv=751797. (e) A mouse brain tissue sections (n = 1) from the hippocampus level was mounted onto an ITO slide and sprayed FMP-10. The area delimited by a red line demarcates the region of interest imaged with MALDI-MSI. (f) Targeted In Situ Sequencing data demonstrate similar rolling circle product (RCP) density generated from MALDI-MSI processed region (upper right panel) and non-processed region (lower right panel) for demarcated regions of interest in the mouse coronal section (n = 1). Targeted ISS simultaneously probed for housekeeping gene, Gapdh labeled in Magenta (Cy5), and a panel of five control genes - Foxj1, Plp1, Lamp5, Rorb and Kcnip2 that are labeled in Cyan (AF750). (g) Mean Cy5 and AF750 fluorescence intensity of rolling circle products in tissue areas imaged or not with MALDI-MSI.The results shown in panels (E-G) belong to one tissue section from n = 1 biologically independent sample examined over one independent experiment. The number of RCPs detected in the MALDI-MSI processed region in AF750 and Cy5 and the number of RCPs detected in the non-processed region in AF750 and Cy5 respectively, which the statistics is derived from, are the following: n = 3830,n = 18231, n = 3051,n = 18193. The lower and upper hinges of the boxplot correspond to the first and third quartiles (the 25th and 75th percentiles), the central white dot corresponds to the median, the upper and lower whiskers extend from the hinge to the maximum or minimum respectively.

Article Snippet: Visium Spatial Gene Expression and Tissue Optimization slides, with the exception of the human postmortem sample, were processed according to the corresponding latest versions of the 10X Genomics protocols (Visium Spatial Gene Expression Reagent Kits—Tissue Optimization User Guide, document CG000238 Rev E, 10X Genomics, (February 2022); Visium Spatial Gene Expression Reagent Kits—User Guide, document CG000239 Rev F, 10X Genomics, (January 2022) and Methanol Fixation, H&E Staining and Imaging for Visium Spatial Protocols, document CG000160 Rev C, 10X Genomics), without any modification.

Techniques: Fluorescence, Microscopy, Standard Deviation, Derivative Assay, In Situ, Sequencing, Generated, Labeling, Control

Violin plots and box plots illustrating the number of unique genes per spot (a) and the number of unique molecular identifiers (UMIs) per spot (b) across biological conditions of the mouse striatum data (n = 9). The numbers of spots per section from which the statistics is derived are the same for the corresponding sections in panels A and B, and are the following: V-iCTRL.FMP10.mPD3.8 = 3017, V-iCTRL.nM.mPD3.3 = 3163, SMA.9AA.mPD3.4 = 2913, SMA.DHB.mPD3.1 = 2856, SMA.DHB.mPD3.2 = 3002, SMA.FMP10.mPD1.5 = 2675, SMA.FMP10.mPD3.6 = 3120, SMA.FMP10.mPD4.7 = 2918, VISIUM.mPD3.9 = 3116. n = 9 sections examined over 3 biologically independent samples. Violin plots and box plots illustrating the number of unique genes per spot (c) and the number of unique molecular identifiers (UMIs) per spot (d) of the human striatum data (n = 1). The human sample H&E was used as a legend to indicate the four capture areas A-D. The numbers of spots per capture area from which the statistics is derived are the same for corresponding sections in panels C and D and are the following: A = 4770, B = 4875, C = 4740, D = 4387. n = 4 capture areas examined over 1 biologically independent sample. For all boxplots presented in (A-D) the lower and upper hinges of the boxplot correspond to the first and third quartiles (the 25th and 75th percentiles), the central line corresponds to the median, the upper and lower whiskers extend from the hinge to the largest or smallest value respectively no further than 1.5 times the inter-quartile range, data beyond the end of the whiskers are plotted individually as black dots. On the right, spatial featureplot representing the number of genes per spot and the number of UMIs per spot of a representative capture area (that is, capture area A). (e) Sequencing metrics: i) Gene body coverage plot illustrating the sequencing coverage at different percentiles of gene body for all the genes in the quality control dataset; ii) sequencing saturation as a function of mean reads per spot; iii) median genes per spot as a function of mean reads per spot. (f) RNA integrity plots of mouse and human post-mortem samples.

Journal: Nature Biotechnology

Article Title: Spatial multimodal analysis of transcriptomes and metabolomes in tissues

doi: 10.1038/s41587-023-01937-y

Figure Lengend Snippet: Violin plots and box plots illustrating the number of unique genes per spot (a) and the number of unique molecular identifiers (UMIs) per spot (b) across biological conditions of the mouse striatum data (n = 9). The numbers of spots per section from which the statistics is derived are the same for the corresponding sections in panels A and B, and are the following: V-iCTRL.FMP10.mPD3.8 = 3017, V-iCTRL.nM.mPD3.3 = 3163, SMA.9AA.mPD3.4 = 2913, SMA.DHB.mPD3.1 = 2856, SMA.DHB.mPD3.2 = 3002, SMA.FMP10.mPD1.5 = 2675, SMA.FMP10.mPD3.6 = 3120, SMA.FMP10.mPD4.7 = 2918, VISIUM.mPD3.9 = 3116. n = 9 sections examined over 3 biologically independent samples. Violin plots and box plots illustrating the number of unique genes per spot (c) and the number of unique molecular identifiers (UMIs) per spot (d) of the human striatum data (n = 1). The human sample H&E was used as a legend to indicate the four capture areas A-D. The numbers of spots per capture area from which the statistics is derived are the same for corresponding sections in panels C and D and are the following: A = 4770, B = 4875, C = 4740, D = 4387. n = 4 capture areas examined over 1 biologically independent sample. For all boxplots presented in (A-D) the lower and upper hinges of the boxplot correspond to the first and third quartiles (the 25th and 75th percentiles), the central line corresponds to the median, the upper and lower whiskers extend from the hinge to the largest or smallest value respectively no further than 1.5 times the inter-quartile range, data beyond the end of the whiskers are plotted individually as black dots. On the right, spatial featureplot representing the number of genes per spot and the number of UMIs per spot of a representative capture area (that is, capture area A). (e) Sequencing metrics: i) Gene body coverage plot illustrating the sequencing coverage at different percentiles of gene body for all the genes in the quality control dataset; ii) sequencing saturation as a function of mean reads per spot; iii) median genes per spot as a function of mean reads per spot. (f) RNA integrity plots of mouse and human post-mortem samples.

Article Snippet: Visium Spatial Gene Expression and Tissue Optimization slides, with the exception of the human postmortem sample, were processed according to the corresponding latest versions of the 10X Genomics protocols (Visium Spatial Gene Expression Reagent Kits—Tissue Optimization User Guide, document CG000238 Rev E, 10X Genomics, (February 2022); Visium Spatial Gene Expression Reagent Kits—User Guide, document CG000239 Rev F, 10X Genomics, (January 2022) and Methanol Fixation, H&E Staining and Imaging for Visium Spatial Protocols, document CG000160 Rev C, 10X Genomics), without any modification.

Techniques: Derivative Assay, Sequencing, Control

(a) Scatterplots of log 10 gene counts of SMA-SRT data vs. stand-alone Visium data. The red line highlights a 1-to-1 relationship, whereas the dashed green and blue lines highlight a log 10 0.5 or −0.5 relationship. (b) Stacked barplot illustrating the percentage of genes with log 10 higher, lower or within the log 10 fold change range −0.5-0.5. The percentages inside the gray bars illustrate the percentages of peaks with absolute log 10 below 0.5.

Journal: Nature Biotechnology

Article Title: Spatial multimodal analysis of transcriptomes and metabolomes in tissues

doi: 10.1038/s41587-023-01937-y

Figure Lengend Snippet: (a) Scatterplots of log 10 gene counts of SMA-SRT data vs. stand-alone Visium data. The red line highlights a 1-to-1 relationship, whereas the dashed green and blue lines highlight a log 10 0.5 or −0.5 relationship. (b) Stacked barplot illustrating the percentage of genes with log 10 higher, lower or within the log 10 fold change range −0.5-0.5. The percentages inside the gray bars illustrate the percentages of peaks with absolute log 10 below 0.5.

Article Snippet: Visium Spatial Gene Expression and Tissue Optimization slides, with the exception of the human postmortem sample, were processed according to the corresponding latest versions of the 10X Genomics protocols (Visium Spatial Gene Expression Reagent Kits—Tissue Optimization User Guide, document CG000238 Rev E, 10X Genomics, (February 2022); Visium Spatial Gene Expression Reagent Kits—User Guide, document CG000239 Rev F, 10X Genomics, (January 2022) and Methanol Fixation, H&E Staining and Imaging for Visium Spatial Protocols, document CG000160 Rev C, 10X Genomics), without any modification.

Techniques:

A: Overview of study design, data modalities, and analysis strategies. Single-cell and nucleus RNA-seq (Bayraktar S. et al. ), Multiome, and Visium spatial transcriptomics data were generated from a total of 23 human fetal hearts between the ages of 4 and 20 PCW. Euploid datasets and models were integrated with and mapped to the newly generated Trisomy 21 datasets (13 and 14 PCW). B: UMAP embedding of chromatin accessibility data of 63 cell types of the developing human heart and the great vessels, spread across 14 mid- and 6 coarse-grains. UMAP embedding of the cells based on the chromatin accessibility profile shares similar segregation patterns with the gene expression profile. C-D: Entropy score (Methods) of neighbourhoods of atrial or ventricular cardiomyocytes or myeloid cells. The UMAP embeddings (C) show neighbourhoods (Milo) identified using gene expression data and scVI latent space. The dot size shows the neighbourhood size and the colour shows the entropy score. The box plots (D) indicate the entropy scores of the neighbourhoods in each assigned cell type label. Data points represent neighbourhoods. p -values are provided for the comparison among groups of cell types as indicated (two-sided Kruskal-Wallis test, for multiple comparisons, post hoc analysis with Dunn’s test was performed with adjusting p-values using the Bonferroni method). E: UMAP embedding of estimated cell type abundances (cell2location) of the Visium spots across 22 spatial sections. Spots were annotated based on clustering, estimated abundance of cell types in each cluster, and histological structure as defined by expert annotations using H&E images (Methods). F: Representative Visium sections, which capture the whole heart, with structural annotations. G: Dotplot displaying the estimated fine-grained cell (columns) abundance per tissue structure annotation (rows). Summarised abundances were normalised for each cell type. AV: atrioventricular, AVN: AV node, GV: great vessel, H&E: hematoxylin and eosin, VCS: ventricular conduction system, VCSp: VCS proximal, CCF: common coordinate framework, GRN: gene regulatory network, PCW: post-conception weeks.

Journal: bioRxiv

Article Title: Multiomic analysis reveals developmental dynamics of the human heart in health and disease

doi: 10.1101/2024.04.29.591736

Figure Lengend Snippet: A: Overview of study design, data modalities, and analysis strategies. Single-cell and nucleus RNA-seq (Bayraktar S. et al. ), Multiome, and Visium spatial transcriptomics data were generated from a total of 23 human fetal hearts between the ages of 4 and 20 PCW. Euploid datasets and models were integrated with and mapped to the newly generated Trisomy 21 datasets (13 and 14 PCW). B: UMAP embedding of chromatin accessibility data of 63 cell types of the developing human heart and the great vessels, spread across 14 mid- and 6 coarse-grains. UMAP embedding of the cells based on the chromatin accessibility profile shares similar segregation patterns with the gene expression profile. C-D: Entropy score (Methods) of neighbourhoods of atrial or ventricular cardiomyocytes or myeloid cells. The UMAP embeddings (C) show neighbourhoods (Milo) identified using gene expression data and scVI latent space. The dot size shows the neighbourhood size and the colour shows the entropy score. The box plots (D) indicate the entropy scores of the neighbourhoods in each assigned cell type label. Data points represent neighbourhoods. p -values are provided for the comparison among groups of cell types as indicated (two-sided Kruskal-Wallis test, for multiple comparisons, post hoc analysis with Dunn’s test was performed with adjusting p-values using the Bonferroni method). E: UMAP embedding of estimated cell type abundances (cell2location) of the Visium spots across 22 spatial sections. Spots were annotated based on clustering, estimated abundance of cell types in each cluster, and histological structure as defined by expert annotations using H&E images (Methods). F: Representative Visium sections, which capture the whole heart, with structural annotations. G: Dotplot displaying the estimated fine-grained cell (columns) abundance per tissue structure annotation (rows). Summarised abundances were normalised for each cell type. AV: atrioventricular, AVN: AV node, GV: great vessel, H&E: hematoxylin and eosin, VCS: ventricular conduction system, VCSp: VCS proximal, CCF: common coordinate framework, GRN: gene regulatory network, PCW: post-conception weeks.

Article Snippet: 3’ gene expression libraries and ATAC libraries were prepared according to the manufacturer’s instructions of the Chromium Multiome ATAC+Gene Expression Kits (10x Genomics).

Techniques: RNA Sequencing Assay, Generated, Expressing, Comparison

A: (i) The workflow of the epigenetic stability assessment. Using Multiome data, for each mid-grained cell type, the overlapping neighbourhoods (Milo) were found using gene expression data and scVI latent space (RNA neighbourhoods) or chromatin accessibility data and peakVI latet space (ATAC neighbourhoods). For each RNA neighbourhood, the entropy of the distribution of corresponding nuclei across the ATAC neighbourhoods was calculated. Data points represent neighbourhoods. (ii) Example distribution of two RNA neighbourhoods in the ATAC space (UMAP embedding based on peakVI latent space) are shown. Data points represent cells. RNA neighbourhood-63 shows greater scattered distribution in the ATAC space and a higher entropy score (0.53), suggesting that the neighbourhood cells are epigenetically unstable and potentially in the process of transitioning to another state. B: Entropy score (plot on the left of each mid-grained cell type) or assigned fine-grained cell type labels (plot on the right) projected on the RNA space (UMAP embedding based on scVI latent space). Data points represent RNA neighbourhoods, and the dot size shows the neighbourhood size.

Journal: bioRxiv

Article Title: Multiomic analysis reveals developmental dynamics of the human heart in health and disease

doi: 10.1101/2024.04.29.591736

Figure Lengend Snippet: A: (i) The workflow of the epigenetic stability assessment. Using Multiome data, for each mid-grained cell type, the overlapping neighbourhoods (Milo) were found using gene expression data and scVI latent space (RNA neighbourhoods) or chromatin accessibility data and peakVI latet space (ATAC neighbourhoods). For each RNA neighbourhood, the entropy of the distribution of corresponding nuclei across the ATAC neighbourhoods was calculated. Data points represent neighbourhoods. (ii) Example distribution of two RNA neighbourhoods in the ATAC space (UMAP embedding based on peakVI latent space) are shown. Data points represent cells. RNA neighbourhood-63 shows greater scattered distribution in the ATAC space and a higher entropy score (0.53), suggesting that the neighbourhood cells are epigenetically unstable and potentially in the process of transitioning to another state. B: Entropy score (plot on the left of each mid-grained cell type) or assigned fine-grained cell type labels (plot on the right) projected on the RNA space (UMAP embedding based on scVI latent space). Data points represent RNA neighbourhoods, and the dot size shows the neighbourhood size.

Article Snippet: 3’ gene expression libraries and ATAC libraries were prepared according to the manufacturer’s instructions of the Chromium Multiome ATAC+Gene Expression Kits (10x Genomics).

Techniques: Expressing