Literature DB >> 32940008

Single-cell RNA sequencing in Drosophila: Technologies and applications.

Hongjie Li1.   

Abstract

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cell states and functions at the single-cell level. It has greatly revolutionized transcriptomic studies in many life science research fields, such as neurobiology, immunology, and developmental biology. With the fast development of both experimental platforms and bioinformatics approaches over the past decade, scRNA-seq is becoming economically feasible and experimentally practical for many biomedical laboratories. Drosophila has served as an excellent model organism for dissecting cellular and molecular mechanisms that underlie tissue development, adult cell function, disease, and aging. The recent application of scRNA-seq methods to Drosophila tissues has led to a number of exciting discoveries. In this review, I will provide a summary of recent scRNA-seq studies in Drosophila, focusing on technical approaches and biological applications. I will also discuss current challenges and future opportunities of making new discoveries using scRNA-seq in Drosophila. This article is categorized under:   Technologies > Analysis of the Transcriptome.
© 2020 Wiley Periodicals LLC.

Entities:  

Keywords:  drosophila; single-cell RNA sequencing

Mesh:

Year:  2020        PMID: 32940008      PMCID: PMC7960577          DOI: 10.1002/wdev.396

Source DB:  PubMed          Journal:  Wiley Interdiscip Rev Dev Biol        ISSN: 1759-7684            Impact factor:   5.814


  129 in total

1.  Full-length RNA-seq from single cells using Smart-seq2.

Authors:  Simone Picelli; Omid R Faridani; Asa K Björklund; Gösta Winberg; Sven Sagasser; Rickard Sandberg
Journal:  Nat Protoc       Date:  2014-01-02       Impact factor: 13.491

2.  Single cell transcriptomic landscapes of pattern formation, proliferation and growth in Drosophila wing imaginal discs.

Authors:  Mingxi Deng; Ying Wang; Lina Zhang; Yang Yang; Shengshuo Huang; Jiguang Wang; Hao Ge; Toyotaka Ishibashi; Yan Yan
Journal:  Development       Date:  2019-09-20       Impact factor: 6.868

3.  A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord.

Authors:  Aaron M Allen; Megan C Neville; Sebastian Birtles; Vincent Croset; Christoph Daniel Treiber; Scott Waddell; Stephen F Goodwin
Journal:  Elife       Date:  2020-04-21       Impact factor: 8.140

4.  Genome-wide detection of single-nucleotide and copy-number variations of a single human cell.

Authors:  Chenghang Zong; Sijia Lu; Alec R Chapman; X Sunney Xie
Journal:  Science       Date:  2012-12-21       Impact factor: 47.728

5.  Proteomics of protein trafficking by in vivo tissue-specific labeling.

Authors:  Amanda S Meyer; Dan Wang; Namrata D Udeshi; Ilia A Droujinine; Yanhui Hu; David Rocco; Jill A McMahon; Rui Yang; JinJin Guo; Luye Mu; Dominique K Carey; Tanya Svinkina; Rebecca Zeng; Tess Branon; Areya Tabatabai; Justin A Bosch; John M Asara; Alice Y Ting; Steven A Carr; Andrew P McMahon; Norbert Perrimon
Journal:  Nat Commun       Date:  2021-04-22       Impact factor: 14.919

6.  Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics.

Authors:  Vincent Croset; Christoph D Treiber; Scott Waddell
Journal:  Elife       Date:  2018-04-19       Impact factor: 8.140

Review 7.  A Single-Cell Sequencing Guide for Immunologists.

Authors:  Peter See; Josephine Lum; Jinmiao Chen; Florent Ginhoux
Journal:  Front Immunol       Date:  2018-10-23       Impact factor: 7.561

8.  A GAL4-driver line resource for Drosophila neurobiology.

Authors:  Arnim Jenett; Gerald M Rubin; Teri-T B Ngo; David Shepherd; Christine Murphy; Heather Dionne; Barret D Pfeiffer; Amanda Cavallaro; Donald Hall; Jennifer Jeter; Nirmala Iyer; Dona Fetter; Joanna H Hausenfluck; Hanchuan Peng; Eric T Trautman; Robert R Svirskas; Eugene W Myers; Zbigniew R Iwinski; Yoshinori Aso; Gina M DePasquale; Adrianne Enos; Phuson Hulamm; Shing Chun Benny Lam; Hsing-Hsi Li; Todd R Laverty; Fuhui Long; Lei Qu; Sean D Murphy; Konrad Rokicki; Todd Safford; Kshiti Shaw; Julie H Simpson; Allison Sowell; Susana Tae; Yang Yu; Christopher T Zugates
Journal:  Cell Rep       Date:  2012-10-11       Impact factor: 9.423

9.  Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling.

Authors:  Susanne Nichterwitz; Geng Chen; Julio Aguila Benitez; Marlene Yilmaz; Helena Storvall; Ming Cao; Rickard Sandberg; Qiaolin Deng; Eva Hedlund
Journal:  Nat Commun       Date:  2016-07-08       Impact factor: 14.919

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  13 in total

1.  Mathematical model and genomics construction of developmental biology patterns using digital image technology.

Authors:  Shiwei Ni; Fei Chen; Guolong Chen; Yufeng Yang
Journal:  Front Genet       Date:  2022-08-10       Impact factor: 4.772

2.  Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

Authors:  Hongjie Li; Jasper Janssens; Maxime De Waegeneer; Sai Saroja Kolluru; Kristofer Davie; Vincent Gardeux; Wouter Saelens; Fabrice P A David; Maria Brbić; Katina Spanier; Jure Leskovec; Colleen N McLaughlin; Qijing Xie; Robert C Jones; Katja Brueckner; Jiwon Shim; Sudhir Gopal Tattikota; Frank Schnorrer; Katja Rust; Todd G Nystul; Zita Carvalho-Santos; Carlos Ribeiro; Soumitra Pal; Sharvani Mahadevaraju; Teresa M Przytycka; Aaron M Allen; Stephen F Goodwin; Cameron W Berry; Margaret T Fuller; Helen White-Cooper; Erika L Matunis; Stephen DiNardo; Anthony Galenza; Lucy Erin O'Brien; Julian A T Dow; Heinrich Jasper; Brian Oliver; Norbert Perrimon; Bart Deplancke; Stephen R Quake; Liqun Luo; Stein Aerts; Devika Agarwal; Yasir Ahmed-Braimah; Michelle Arbeitman; Majd M Ariss; Jordan Augsburger; Kumar Ayush; Catherine C Baker; Torsten Banisch; Katja Birker; Rolf Bodmer; Benjamin Bolival; Susanna E Brantley; Julie A Brill; Nora C Brown; Norene A Buehner; Xiaoyu Tracy Cai; Rita Cardoso-Figueiredo; Fernando Casares; Amy Chang; Thomas R Clandinin; Sheela Crasta; Claude Desplan; Angela M Detweiler; Darshan B Dhakan; Erika Donà; Stefanie Engert; Swann Floc'hlay; Nancy George; Amanda J González-Segarra; Andrew K Groves; Samantha Gumbin; Yanmeng Guo; Devon E Harris; Yael Heifetz; Stephen L Holtz; Felix Horns; Bruno Hudry; Ruei-Jiun Hung; Yuh Nung Jan; Jacob S Jaszczak; Gregory S X E Jefferis; Jim Karkanias; Timothy L Karr; Nadja Sandra Katheder; James Kezos; Anna A Kim; Seung K Kim; Lutz Kockel; Nikolaos Konstantinides; Thomas B Kornberg; Henry M Krause; Andrew Thomas Labott; Meghan Laturney; Ruth Lehmann; Sarah Leinwand; Jiefu Li; Joshua Shing Shun Li; Kai Li; Ke Li; Liying Li; Tun Li; Maria Litovchenko; Han-Hsuan Liu; Yifang Liu; Tzu-Chiao Lu; Jonathan Manning; Anjeli Mase; Mikaela Matera-Vatnick; Neuza Reis Matias; Caitlin E McDonough-Goldstein; Aaron McGeever; Alex D McLachlan; Paola Moreno-Roman; Norma Neff; Megan Neville; Sang Ngo; Tanja Nielsen; Caitlin E O'Brien; David Osumi-Sutherland; Mehmet Neset Özel; Irene Papatheodorou; Maja Petkovic; Clare Pilgrim; Angela Oliveira Pisco; Carolina Reisenman; Erin Nicole Sanders; Gilberto Dos Santos; Kristin Scott; Aparna Sherlekar; Philip Shiu; David Sims; Rene V Sit; Maija Slaidina; Harold E Smith; Gabriella Sterne; Yu-Han Su; Daniel Sutton; Marco Tamayo; Michelle Tan; Ibrahim Tastekin; Christoph Treiber; David Vacek; Georg Vogler; Scott Waddell; Wanpeng Wang; Rachel I Wilson; Mariana F Wolfner; Yiu-Cheung E Wong; Anthony Xie; Jun Xu; Shinya Yamamoto; Jia Yan; Zepeng Yao; Kazuki Yoda; Ruijun Zhu; Robert P Zinzen
Journal:  Science       Date:  2022-03-04       Impact factor: 63.714

3.  Systematic expression profiling of Dpr and DIP genes reveals cell surface codes in Drosophila larval motor and sensory neurons.

Authors:  Yupu Wang; Meike Lobb-Rabe; James Ashley; Purujit Chatterjee; Veera Anand; Hugo J Bellen; Oguz Kanca; Robert A Carrillo
Journal:  Development       Date:  2022-05-19       Impact factor: 6.862

Review 4.  Methods and tools for spatial mapping of single-cell RNAseq clusters in Drosophila.

Authors:  Stephanie E Mohr; Sudhir Gopal Tattikota; Jun Xu; Jonathan Zirin; Yanhui Hu; Norbert Perrimon
Journal:  Genetics       Date:  2021-04-15       Impact factor: 4.562

5.  Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila.

Authors:  Colleen N McLaughlin; Maria Brbić; Qijing Xie; Tongchao Li; Felix Horns; Sai Saroja Kolluru; Justus M Kebschull; David Vacek; Anthony Xie; Jiefu Li; Robert C Jones; Jure Leskovec; Stephen R Quake; Liqun Luo; Hongjie Li
Journal:  Elife       Date:  2021-02-08       Impact factor: 8.140

6.  Single-Cell RNA Sequencing Analysis of the Drosophila Larval Ventral Cord.

Authors:  Tho Huu Nguyen; Rosario Vicidomini; Saumitra Dey Choudhury; Steven L Coon; James Iben; Thomas Brody; Mihaela Serpe
Journal:  Curr Protoc       Date:  2021-02

7.  DRscDB: A single-cell RNA-seq resource for data mining and data comparison across species.

Authors:  Yanhui Hu; Sudhir Gopal Tattikota; Yifang Liu; Aram Comjean; Yue Gao; Corey Forman; Grace Kim; Jonathan Rodiger; Irene Papatheodorou; Gilberto Dos Santos; Stephanie E Mohr; Norbert Perrimon
Journal:  Comput Struct Biotechnol J       Date:  2021-04-11       Impact factor: 7.271

8.  Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons.

Authors:  Qijing Xie; Maria Brbic; Felix Horns; Sai Saroja Kolluru; Robert C Jones; Jiefu Li; Anay R Reddy; Anthony Xie; Sayeh Kohani; Zhuoran Li; Colleen N McLaughlin; Tongchao Li; Chuanyun Xu; David Vacek; David J Luginbuhl; Jure Leskovec; Stephen R Quake; Liqun Luo; Hongjie Li
Journal:  Elife       Date:  2021-01-11       Impact factor: 8.140

Review 9.  Micromanagement of Drosophila Post-Embryonic Development by Hox Genes.

Authors:  Alexandra D Buffry; Alistair P McGregor
Journal:  J Dev Biol       Date:  2022-02-18

10.  Single-Cell Profiling of Tumor Microenvironment Heterogeneity in Osteosarcoma Identifies a Highly Invasive Subcluster for Predicting Prognosis.

Authors:  Junfeng Guo; Hong Tang; Pan Huang; Junfeng Guo; Youxing Shi; Chengsong Yuan; Taotao Liang; Kanglai Tang
Journal:  Front Oncol       Date:  2022-04-06       Impact factor: 5.738

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