EMBO Practical Course
MicroRNA profiling: From In-Situ Hybridization to New Gen Sequencing
EMBL Monterotondo, Italy Saturday 10 April - Friday 16 April 2010
Programme
We will start every morning at 9 am. The course ends on Friday 16 April at around 4 pm.
Preliminary Programme
|
Saturday 10 April 2010 |
|
|---|---|
| 09.00 | Welcome and Introduction |
| Blackboard session: microarray protocol | |
| Wet lab: sample labelling with modified Exiqon protocol | |
| Blackboards: Introduction to in situ | |
| Lunch | |
| Wet lab: RNA Precipitation | |
| Effect of RNA degradation on miRNAs profile | |
| Blackboard session: introduction to hybridization | |
| Wet lab: cleaning the labelled samples and starting the hybridization of the miRCURY LNA arrays | |
| The small RNA zoo: "miRNA, piRNA and siRNA in C. elegans development." | |
| Summary of the day, participants' presentations, wine & beer | |
| Dinner at the hotel | |
|
Sunday 11 April 2010 |
|
| 09.00 | miRNAs and methods used for their profiling |
| Wet Lab: participants carry on the first step of the washing, afterwards Sabine and David take over washing and scanning | |
| Afternoon in Rome | |
| Return to Monterotondo | |
|
Monday 12 April 2010 |
|
| 09.00 | Web Lab: In situ hybridization (Introduction) |
| Round table/Troubleshooting on microarray hybridization, manual or automated processing | |
| miRNAs, mRNAs (the good, the bad and the rest) | |
| Lunch | |
| Introduction to Luminex | |
| In situ hybridization/ microRNA target prediction | |
| Summary of the day, participants’ presentations, wine & beer | |
| Dinner at the hotel | |
|
Tuesday 13 April 2010 |
|
| 09.00 | Blackboard session & Wet lab: Luminex protocol |
| Practical: Bead based high-throughput miRNA assays | |
| QC of RNA Quality, effect on data analysis | |
| Lunch | |
| Luminex data analysis | |
| Bioinformatics and Biologists | |
| Talk about in situ, qPCR and next generation sequencing | |
| Summary of the day, participants’ presentations, wine & beer | |
| Dinner at the hotel | |
|
Wednesday 14 April 2010 |
|
| 09.00 | In Situ Hybridization, washing, staining |
| Analysis of array data using R & BioConductorLectures and practical workshop about analysis of miRCURY LNA arrays using BioConductorTopics including preprocessing, normalization, detecting regulated genes using various methods. | |
| In situ hybridization: miRNA expression visualization | |
| Lunch | |
| Complete analysis of the microarray data, continued | |
| SOLiD analysis of miRNA | |
| Introduction to qPCR normalization, REST | |
| Summary of the day | |
| Freetime in the evening | |
|
Thursday 15 April 2010 |
|
| 09:00 | Blackboard session & wet lab: cDNA preparation |
| The qPCR system and LNA/TaqMan methods | |
| Wet lab: qPCR actual run | |
| Lunch | |
| Round table/troubleshooting in situ hybridizations | |
| Practical analysis on qPCR data | |
| Summary of the day, participants’ presentations | |
| BBQ Dinner (weather dependent) | |
|
Friday 16 April 2010 |
|
| 09.00 | Ancient miRNAs and evolution of tissue identity |
| Data analysis and their interpretation | |
| Lunch | |
| Single cell resolution of miRNA expression in vivo | |
| More data analysis, troubleshooting | |
| Integration of miRNA data from various sources and making sense out of them | |
| Conclusive & concluding remarks | |