Protocols provided by JGI and the JGI user community. JGI sample QC protocols can be found here.
DNA preparation protocols:
- JGI Bacterial DNA isolation CTAB-2012
- Isolation_of_Genomic_DNA_from_Phytophthora
- Isolation_of_Melampsora_Nuclear_DNA
- DNA_Isolation_of_Plant Nuclear_DNA
- Populus nuclear DNA purification with Qiagen
- DNA_extraction_from_Activated_Sludge
- Cloning of High Molecular Weight eDNA (soil)
- RNaseA_DNA_Cleanup
- eDNA _purification (removal of humics)
- High Molecular Weight DNA Extraction from Soil
- http://1000.fungalgenomes.org/home/protocols/
- High Molecular Weight DNA extraction protocols from PacBio: https://extractdnaforpacbio.com/
Tips for High Molecular Weight DNA extraction:
- DNA Extraction 101 – tips, kits, and protocols (from PacBio)
- Guidance for sample collection and storage (from PacBio)
- Best practices for High Molecular Weight DNA extraction and quality control (from PacBio)
RNA preparation protocols:
- DNase Treatment of Total RNA
- LiCl RNA cleanup
- RNA Isolation from LCM samples
- Chlamydomonas large-scale RNA extraction
The JGI has conducted studies to verify that technical replicates are not needed for RNASeq experiments. The results of those studies are detailed in this presentation: