Protocols

Live RNA Imaging Strategies in C. elegans

2021 Worm Meeting Workshop on live RNA Imaging Strategies in C. elegans

Fluorescence Recovery after Photobleaching (FRAP) in worms:

Check out Laura's (joint PhD student between Ercan & Preibisch labs) FRAP protocol at protocols.io

Chromatin Immunoprecipitation (ChIP-seq) & RNA-seq in worms:

Thoughts on spike in ChIP-seq 

2015 Worm Meeting ChIP-seq & RNA-seq workshop materials: 2015 International Worm Meeting Workshop

2016 DNA-protein binding workshop materials: 2016 Spain Workshop for Genie

Our analysis scripts are at: https://github.com/ercanlab 

Note that nowadays we have been using a nicely documented tool called DeepTools for ChIP-seq processing and analysis.

modENCODE related: 

modENCODE histone antibody database for antibody selection: Antibody database

Commercially available antibodies from modENCODE: Novus antibodies

modENCODE chromatin data sets and modENCODE transcription factor data sets

new modENCODE TF binding database: modENCODE TF group

Teaching: DSI-2016

Current protocols from Ercan lab:

Note about growing worms for ChIP: In the past we grew worms in liquid. Nowadays we use 10 cm NGM plates.  They stay much cleaner, and you can scale up by simply increasing the number of plates. 

Note about ChIP extract preparation: modENCODE TF group does not freeze-grind larvae. We found that overgrinding leads to low signal in ChIPs. In v9 we use live crosslinked larvae and do not grind for making ChIP extract.