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A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes.
Grancharova, Tanya; Gerbin, Kaytlyn A; Rosenberg, Alexander B; Roco, Charles M; Arakaki, Joy E; DeLizo, Colette M; Dinh, Stephanie Q; Donovan-Maiye, Rory M; Hirano, Matthew; Nelson, Angelique M; Tang, Joyce; Theriot, Julie A; Yan, Calysta; Menon, Vilas; Palecek, Sean P; Seelig, Georg; Gunawardane, Ruwanthi N.
Afiliação
  • Grancharova T; Allen Institute for Cell Science, Seattle, WA, USA.
  • Gerbin KA; Allen Institute for Cell Science, Seattle, WA, USA.
  • Rosenberg AB; Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.
  • Roco CM; , Parse Biosciences, Seattle, WA, USA.
  • Arakaki JE; , Parse Biosciences, Seattle, WA, USA.
  • DeLizo CM; Department of Bioengineering, University of Washington, Seattle, WA, USA.
  • Dinh SQ; Allen Institute for Cell Science, Seattle, WA, USA.
  • Donovan-Maiye RM; Allen Institute for Cell Science, Seattle, WA, USA.
  • Hirano M; Allen Institute for Cell Science, Seattle, WA, USA.
  • Nelson AM; Allen Institute for Cell Science, Seattle, WA, USA.
  • Tang J; Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.
  • Theriot JA; Allen Institute for Cell Science, Seattle, WA, USA.
  • Yan C; Allen Institute for Cell Science, Seattle, WA, USA.
  • Menon V; Allen Institute for Cell Science, Seattle, WA, USA.
  • Palecek SP; Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
  • Seelig G; Allen Institute for Cell Science, Seattle, WA, USA.
  • Gunawardane RN; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
Sci Rep ; 11(1): 15845, 2021 08 04.
Article em En | MEDLINE | ID: mdl-34349150
We performed a comprehensive analysis of the transcriptional changes occurring during human induced pluripotent stem cell (hiPSC) differentiation to cardiomyocytes. Using single cell RNA-seq, we sequenced > 20,000 single cells from 55 independent samples representing two differentiation protocols and multiple hiPSC lines. Samples included experimental replicates ranging from undifferentiated hiPSCs to mixed populations of cells at D90 post-differentiation. Differentiated cell populations clustered by time point, with differential expression analysis revealing markers of cardiomyocyte differentiation and maturation changing from D12 to D90. We next performed a complementary cluster-independent sparse regression analysis to identify and rank genes that best assigned cells to differentiation time points. The two highest ranked genes between D12 and D24 (MYH7 and MYH6) resulted in an accuracy of 0.84, and the three highest ranked genes between D24 and D90 (A2M, H19, IGF2) resulted in an accuracy of 0.94, revealing that low dimensional gene features can identify differentiation or maturation stages in differentiating cardiomyocytes. Expression levels of select genes were validated using RNA FISH. Finally, we interrogated differences in cardiac gene expression resulting from two differentiation protocols, experimental replicates, and three hiPSC lines in the WTC-11 background to identify sources of variation across these experimental variables.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Biomarcadores / Diferenciação Celular / Regulação da Expressão Gênica / Miócitos Cardíacos / Células-Tronco Pluripotentes Induzidas / Transcriptoma Idioma: En Ano de publicação: 2021 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Biomarcadores / Diferenciação Celular / Regulação da Expressão Gênica / Miócitos Cardíacos / Células-Tronco Pluripotentes Induzidas / Transcriptoma Idioma: En Ano de publicação: 2021 Tipo de documento: Article