Protocol for the preservation of animal tissues for RNA and DNA and Metabolomics samples in the presence or absence of liquid nitrogen and -80 freezers. This provides an option for remote field collection protocol.

Set up dual input temperature control code for Apex through Apex Fusion interface

Submission of Montipora capitata spawning gene expression sequence data from 18 RNASeq libraries to NCBI SRA

Examination of DML pattern clusters across treatment

Extracted DNA from Larval Geoduck Tissue frozen at -80°C and stored in RNALater

Results from geoduck juvenile RRBS library pool1 from batch 1 back from Genewiz

Results from geoduck juvenile RRBS library pool1 from batch 1 back from Genewiz

Prepping 40 RRBS libraries for geoduck juvenile OA acclimatization study.

Prepping remaining 76 RRBS libraries for geoduck juvenile OA acclimatization study.

RNA Extractions from Juvenile Geoduck samples in Gallardo-Escárate Lab

Prepping RRBS libraries for geoduck juvenile OA acclimatization study.

Testing RRBS protocol using MSPI cutting, BS treatment, and Illumina Trueseq DNA methylation kit

Using Bismark to extract CpG methylation information from Ostrea lurida sequence data Oly Oyster Methylation Project

Split geoduck juvenile samples from second exposure period into 3 portions for RNA and DNA extraction

List of November 2016 Goals

Extracted DNA from Juvenile Geoduck Tissue frozen at -80°C Extracted DNA from Larval Geoduck Tissue frozen at -80°C and stored in RNALater

Extracted DNA from Juvenile Geoduck Tissue frozen at -80°C

Extracted DNA from Juvenile Geoduck Tissue frozen at -80°C

Extracted DNA from Juvenile Geoduck Tissue frozen at -80°C

Extracted DNA from Juvenile Geoduck Tissue previously homogenized using the Sample Homogenization Protocol

Tested RNA extractions using Ambion RiboPure Kit Protocol RNA Extraction Protocol RiboPure Kit

Protocol for the extraction of total RNA for use in QPCR and Next Generation Sequencing. Yeilds total RNA that has been DNAse treated and is ready for downstream applications.

Tested RNA extractions for improving quality and identifying if peaks prior to major ribosomal peak are degradation or RNA from gut contents

20160901-20160912 Homogenization of juvenile geoduck samples for use in nucleic acid extractions

20160829-20160830 Testing for improved yield of RNA with no genomic DNA contamination and for removal of rRNA through one round of polyA selection on total RNA

20160824-20160829 Homogenization of juvenile geoduck samples for use in nucleic acid extractions

Protocol for the extraction of total RNA for use in QPCR and Next Generation Sequencing. Yeilds total RNA that has been DNAse treated and is ready for downstream applications.

Protocol for the quantification of RNA. Provides RNA sample concentration

Protocol for the quantification of genomic DNA. Provides DNA sample concentration

Protocol for the homogenization of tissues by grinding on liquid nitrogen to maintain nucleic acid integrity and produce a homogenous tissue distribution for each downstream assay. Yields tissue powder that is stored at -80°C for downstream analyses.

Protocol for the extraction of genomic DNA for use in PCR and Next Generation Sequencing. Yeilds total DNA that has been proteinase and RNase treated and is ready for downstream applications.

Protocol for checking the quality of RNA. Provides RNA integrity number and microgel to assess degradation and DNA contamination.

Protocol for the preservation of animal tissues for RNA and DNA extraction in the absence of liquid nitrogen and -80 freezers (i.e., remote field collection protocol)

Protocol for the removal of coral tissue from the skeleton using an airbrush. Yields tissue slurry that can be used for biological assays and clean skeleton that can be used for surface area measurement.

Objective:Test quantity and quality of RNA extracted from fresh coral samples of 3 species (Montipora capitata, Porites compressa, and Pocillopora damicornis). This protocol includes a purification column which has not been used in the previous extractions and should increase quality.