| Chapter title |
Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos
|
|---|---|
| Chapter number | 9 |
| Book title |
RNA Detection
|
| Published in |
Methods in molecular biology, January 2018
|
| DOI | 10.1007/978-1-4939-7213-5_9 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-7212-8, 978-1-4939-7213-5
|
| Authors |
L. Carine Stapel, Coleman Broaddus, Nadine L. Vastenhouw |
| Abstract |
Single molecule fluorescence in situ hybridization (smFISH) is a method to visualize single mRNA molecules. When combined with cellular and nuclear segmentation, transcripts can be assigned to different cellular compartments resulting in quantitative information on transcript levels at subcellular resolution. The use of smFISH in zebrafish has been limited by the lack of protocols and an automated image analysis pipeline for samples of multicellular organisms. Here we present a protocol for smFISH on zebrafish cryosections. The protocol includes a method to obtain high-quality sections of zebrafish embryos, an smFISH protocol optimized for zebrafish cryosections, and a user-friendly, automated analysis pipeline for cell segmentation and transcript detection. The software is freely available and can be used to analyze sections of any multicellular organism. |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 9 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 2 | 22% |
| Student > Bachelor | 2 | 22% |
| Student > Doctoral Student | 1 | 11% |
| Student > Master | 1 | 11% |
| Professor | 1 | 11% |
| Other | 0 | 0% |
| Unknown | 2 | 22% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 3 | 33% |
| Nursing and Health Professions | 1 | 11% |
| Biochemistry, Genetics and Molecular Biology | 1 | 11% |
| Unknown | 4 | 44% |