Single-cell genomic analysis of human cerebral organoids
| العنوان: | Single-cell genomic analysis of human cerebral organoids |
|---|---|
| المؤلفون: | J. Gray Camp, Sabina Kanton, Barbara Treutlein |
| المساهمون: | Spence, Jason R. |
| المصدر: | Methods in Cell Biology, 159 Human Pluripotent Stem Cell Derived Organoid Models Methods in Cell Biology Methods in Cell Biology-Human Pluripotent Stem Cell Derived Organoid Models |
| بيانات النشر: | Academic Press, 2020. |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | 0303 health sciences, Brain development, Cell, Computational biology, Cerebral organoids, single-cell RNA-Seq, Single-cell ATAC-seq, Data analysis, Biology, Chromatin, Transcriptome, 03 medical and health sciences, medicine.anatomical_structure, Cell culture, medicine, Organoid, Fibroblast, Induced pluripotent stem cell, 030304 developmental biology |
| الوصف: | Investigating early brain development has previously relied on using primary developing brain tissue or two-dimensional cell culture models. Recently, stem cell-derived three-dimensional cell culture systems, collectively called brain organoids, have been developed that can faithfully recapitulate many aspects of early brain development. Together with the ability to reprogram fibroblast or blood cells into induced pluripotent stem cells from humans with neurodevelopmental disorders, this opens new inroads to study patient-specific brain development in a personalized cell culture model. Studying the transcriptomes and regulatory landscape of single cells within brain organoids presents a major advance to understand cell-type specific features and transient states during development, and to link these states to their underlying regulatory logic at high resolution. In this protocol, we describe how to generate single-cell RNA-seq and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data from the same suspension of organoid cells and focus on reducing batch effects by multiplexing multiple individuals in one experiment. Moreover, we outline basic data processing, analysis, and strategies to correct for batch effects, to account for variability in organoids and for integrating gene expression and open chromatin data. ISSN:0091-679X |
| اللغة: | English |
| ردمك: | 978-0-12-821531-9 |
| تدمد: | 0091-679X |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2ecf251aa3f0dd57fe6097114ababd65Test https://hdl.handle.net/20.500.11850/459060Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....2ecf251aa3f0dd57fe6097114ababd65 |
| قاعدة البيانات: | OpenAIRE |
| ردمك: | 9780128215319 |
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| تدمد: | 0091679X |