Chatterjee, Deeptiman, Deng, Wu-Min (2023) Standardization of Single-Cell RNA-Sequencing Analysis Workflow to Study Drosophila Ovary. Methods in Molecular Biology, 2677. pp. 151-171. ISSN 1064-3745
Abstract
Developments in single-cell technology have considerably changed the way we study biology. Significant efforts have been made over the last few years to build comprehensive cell-type-specific transcriptomic atlases for a wide range of tissues in several model organisms in order to discover cell-type-specific markers and drivers of gene expression. One such tissue is the ovary of the fruit-fly Drosophila melanogaster, which is a popular model system with wide-ranging applications in the study of both development and disease. Three independent studies have recently produced comprehensive maps of cell-type-specific gene expression that describe both spatiotemporal regulation of the process of oogenesis and unique transcriptomic profiles of different cell types that constitute the ovary. In this chapter, we outlined the wet-lab protocol that was followed in our recent study for sample preparation and reanalyze the resultant dataset to discuss the benchmarks in data analysis, which are fundamental to comprehensive curation of the single-cell dataset representing the fly ovary.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics > analysis and processing bioinformatics organism description > animal > insect > Drosophila bioinformatics > genomics and proteomics Investigative techniques and equipment organism description > animal Investigative techniques and equipment > assays organism description > animal > insect Investigative techniques and equipment > assays > RNA-seq |
| CSHL Authors: | |
| Communities: | CSHL labs > Dos Santos lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 2023 |
| Date Deposited: | 21 Sep 2023 18:59 |
| Last Modified: | 08 Jan 2024 18:21 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/40954 |
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