Chapter title |
Analysis of Clonal Composition in Human iPSC and ESC and Derived 2D and 3D Differentiated Cultures.
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Chapter number | 414 |
Book title |
Induced Pluripotent Stem (iPS) Cells
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Published in |
Methods in molecular biology, September 2021
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DOI | 10.1007/7651_2021_414 |
Pubmed ID | |
Book ISBNs |
978-1-07-162118-9, 978-1-07-162119-6
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Authors |
Del Olmo, Bernat, Merkurjev, Daria, Yao, Likun, Pinsach-Abuin, Mel Lina, Garcia-Bassets, Ivan, Almenar-Queralt, Angels, del Olmo, Bernat, Pinsach-Abuin, Mel·lina, Olmo, Bernat |
Abstract |
Human induced pluripotent and embryonic stem cell cultures (hiPSC/hESC) are phenotypically heterogeneous and prone to clonal deviations during subculturing and differentiation. Clonal deviations often emerge unnoticed, but they can change the biology of the cell culture with a negative impact on experimental reproducibility. Here, we describe a computational workflow to profile the bulk clonal composition in a hiPSC/hESC culture that can also be used to infer clonal deviations. This workflow processes data obtained with two versions of the same method. The two versions-epigenetic and transcriptomic-rely on a mechanism of stochastic H3K4me3 deposition during hiPSC/hESC derivation. This mechanism generates a signature of ten or more H3K4me3-enriched clustered protocadherin (PCDH) promoters distinct in every single cell. The aggregate of single-cell signatures provides an identificatory feature in every hiPSC/hESC line. This feature is stably transmitted to the cell progeny of the culture even after differentiation unless there is a clonal deviation event that changes the internal balance of single-cell signatures. H3K4me3 signatures can be profiled by chromatin immunoprecipitation and next-generation sequencing (ChIP-seq). Alternatively, an equivalent PCDH-expression version can be profiled by RNA-seq in PCDH-expressing hiPSC/hESC-derived cells (such as neurons, astrocytes, and cardiomyocytes; and, in long-term cultures, such as cerebral organoids). Notably, our workflow can also distinguish genetically identical hiPSC/hESC lines derived from the same patient or generated in the same editing process. Together, we propose a method to improve data sharing and reproducibility in the hiPSC and hESC fields. |
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Unknown | 2 | 100% |
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Members of the public | 2 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Unknown | 5 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
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Student > Ph. D. Student | 1 | 20% |
Professor > Associate Professor | 1 | 20% |
Student > Doctoral Student | 1 | 20% |
Unknown | 2 | 40% |
Readers by discipline | Count | As % |
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Biochemistry, Genetics and Molecular Biology | 1 | 20% |
Medicine and Dentistry | 1 | 20% |
Unknown | 3 | 60% |