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(A) Infarcted hearts D1, D2, and D4 after MI were enzymatically digested, FACS sorted (singlets, DAPI−Ter119−) and barcoded for single <t>cell</t> <t>RNA</t> sequencing using custom <t>inDrop</t> barcoding platform (N = 3 biological replicates per day post-MI; 10,666 cells). (B) UMAP of bioinformatically isolated and integrated neutrophils (S100a8, S100a9, Cxcr2, Csf3r)HI. (C) Spearman’s rank correlation coefficient comparing heart and blood neutrophil subsets. (D) Integrated heatmap. (E,F) Distribution of neutrophil subsets by time (data are shown as mean +/− S.E.M). (G) Violin plots of subclustered ISG− and ISG+ cells (D1, D2 and D4 post-MI combined). Top marker gene for each neutrophil subset shown. (H, I) Pseudotime trajectory (Monocle) on ISG− and ISG+ (H) and heatmap of neutrophil maturation and ISG expression vs pseudotime (I) from RetnlgHISiglecfLOW to RetnlgLOWSiglecfHI.
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(A) Infarcted hearts D1, D2, and D4 after MI were enzymatically digested, FACS sorted (singlets, DAPI−Ter119−) and barcoded for single <t>cell</t> <t>RNA</t> sequencing using custom <t>inDrop</t> barcoding platform (N = 3 biological replicates per day post-MI; 10,666 cells). (B) UMAP of bioinformatically isolated and integrated neutrophils (S100a8, S100a9, Cxcr2, Csf3r)HI. (C) Spearman’s rank correlation coefficient comparing heart and blood neutrophil subsets. (D) Integrated heatmap. (E,F) Distribution of neutrophil subsets by time (data are shown as mean +/− S.E.M). (G) Violin plots of subclustered ISG− and ISG+ cells (D1, D2 and D4 post-MI combined). Top marker gene for each neutrophil subset shown. (H, I) Pseudotime trajectory (Monocle) on ISG− and ISG+ (H) and heatmap of neutrophil maturation and ISG expression vs pseudotime (I) from RetnlgHISiglecfLOW to RetnlgLOWSiglecfHI.
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(A) Infarcted hearts D1, D2, and D4 after MI were enzymatically digested, FACS sorted (singlets, DAPI−Ter119−) and barcoded for single cell RNA sequencing using custom inDrop barcoding platform (N = 3 biological replicates per day post-MI; 10,666 cells). (B) UMAP of bioinformatically isolated and integrated neutrophils (S100a8, S100a9, Cxcr2, Csf3r)HI. (C) Spearman’s rank correlation coefficient comparing heart and blood neutrophil subsets. (D) Integrated heatmap. (E,F) Distribution of neutrophil subsets by time (data are shown as mean +/− S.E.M). (G) Violin plots of subclustered ISG− and ISG+ cells (D1, D2 and D4 post-MI combined). Top marker gene for each neutrophil subset shown. (H, I) Pseudotime trajectory (Monocle) on ISG− and ISG+ (H) and heatmap of neutrophil maturation and ISG expression vs pseudotime (I) from RetnlgHISiglecfLOW to RetnlgLOWSiglecfHI.

Journal: Science immunology

Article Title: The myeloid type I interferon response to myocardial infarction begins in bone marrow and is regulated by Nrf2-activated macrophages

doi: 10.1126/sciimmunol.aaz1974

Figure Lengend Snippet: (A) Infarcted hearts D1, D2, and D4 after MI were enzymatically digested, FACS sorted (singlets, DAPI−Ter119−) and barcoded for single cell RNA sequencing using custom inDrop barcoding platform (N = 3 biological replicates per day post-MI; 10,666 cells). (B) UMAP of bioinformatically isolated and integrated neutrophils (S100a8, S100a9, Cxcr2, Csf3r)HI. (C) Spearman’s rank correlation coefficient comparing heart and blood neutrophil subsets. (D) Integrated heatmap. (E,F) Distribution of neutrophil subsets by time (data are shown as mean +/− S.E.M). (G) Violin plots of subclustered ISG− and ISG+ cells (D1, D2 and D4 post-MI combined). Top marker gene for each neutrophil subset shown. (H, I) Pseudotime trajectory (Monocle) on ISG− and ISG+ (H) and heatmap of neutrophil maturation and ISG expression vs pseudotime (I) from RetnlgHISiglecfLOW to RetnlgLOWSiglecfHI.

Article Snippet: Single cell RNA-seq was performed by microfluidic droplet-based encapsulation, barcoding, and library preparation, (inDrop and 10X Genomics) as previously described ( 30 ).

Techniques: RNA Sequencing, Isolation, Hi-C, Marker, Expressing