Attempting TagSeq Protocol Again (Partial) on 4 RNA Samples from Holobiont Project, Doing Each Library Twice with Either New Primers with Increased Concentration or the cDNA Amplification with KAPA HiFi HotStart Mix

Attempting TagSeq Protocol Again (Partial) on 4 RNA Samples from Holobiont Project, Doing Each Library Twice with Either New DTT or New SmartScibe and Buffer

Attempting TagSeq Protocol Again on 4 RNA Samples from Holobiont Project

Testing TagSeq Protocol on 4 RNA Samples from Ariana’s Coral Larvae

Using the Zymo Pico Methyl Seq Library Prep Kit For 1 Re-Do Montipora DNA Samples from KBay Project

Doing a 1 Cycle Reconditioning PCR on KBay WGBS Libraries That Looked Over-Amplified/Overly Broad Peaks

Using the Zymo Pico Methyl Seq Library Prep Kit For 16 Montipora DNA Samples from KBay Project

Using the Zymo Pico Methyl Seq Library Prep Kit For Another 12 Montipora DNA Samples from KBay Project

Dilute and Re-QC WGBS Libraries from This Post Because of High Concentration and Potential Overloading of the TapeStation

Using the Zymo Pico Methyl Seq Library Prep Kit For 12 Montipora DNA Samples from KBay Project

Using Larvae Extraction Protocol on the last 4 of Ariana’s Montipora Coral Recruits on Flash Frozen Plugs

2nd Attempt of HMW DNA Extraction of Fire Coral Stored in DNA/RNA Shield

Genomic Tip High Molecular Weight DNA Extraction Protocol

Using Larvae Extraction Protocol on 5 of Ariana’s Montipora Coral Recruits on Flash Frozen Plugs

Try HMW DNA Extraction of Fire Coral Stored in DNA/RNA Shield

Using Larvae Extraction Protocol on 3 of Ariana’s Montipora Coral Recruits on Flash Frozen Plugs

Using the EpiGentek MethylFlash Global DNA Methylation (5-mC) ELISA Easy Kit (Colormetric) on 8 Bleached and 8 Not Bleached Montipora Fragment DNA from December in HI

Using Larvae Extraction Protocol on 12 of Ariana’s Montipora Coral Larvae Stored in DNA/RNA Shield

Using Larvae Extraction Protocol on 6 of Ariana’s Montipora Coral Larvae Stored in DNA/RNA Shield

Using Larvae Extraction Protocol on 8 of Ariana’s Montipora Coral Larvae Stored in DNA/RNA Shield

Using Larvae Extraction Protocol on 10 of Ariana’s Montipora Coral Larvae Stored in DNA/RNA Shield

Protocol for Coral Larvae/Eggs DNA/RNA Extraction

Using Larvae Extraction Protocol on 4 of Ariana’s Montipora Coral Larvae Stored in DNA/RNA Shield

Re-Testing Biomin Montipora Larvae and Saving Half the Volume for DNA/RNA Extraction

Re-Testing Biomin Montipora Larvae/Eggs for DNA/RNA Extraction

Testing DNA/RNA Extraction and Bead or Pestle Homogenization Protocol on Acropora hyacinthus Larvae

Amplifying mtORF region from HMW Pocillopora Extraction and Sequencing Prep

HMW DNA Extraction of Pocillopora acuta with the Qiagen Genomic Tip

Purity and Integrity Check of RNA Samples from the Biomineralization Project That Were Extracted in 2019 by Erin Chille

2nd Try HMW DNA Extraction for Pac-Bio Sequencing of Porites lobata Flash Frozen Tissue Chunk

Second HMW DNA Extraction for Pac-Bio Sequencing of Pocillopora meandrina Flash Frozen Tissue Chunk

Re-TapeStation the Genomic Tip Porites lobata HMW DNA Extraction Products for Better Visualization

Protocol for PocHistone Amplification and Sanger Sequencing for Determining Pocillopora Species

Low-Salt CTAB DNA Extraction Attempt for HMW DNA from Pocillopora meandrina for Genome Sequencing

Preparing Montipora capitata Sample for Shipping to Dovetail Genomics for PacBio Sequencing and Genome Assembly

Sampling of 2 Pocilloporid Corals From the Aquarium Room, DNA Extraction, mtORF Amplification, and Sanger Sequencing Prep for Species Determination

Trying RNA Extraction for Israel with Zymo Kit for Porites asteroides Samples

HMW DNA Extraction for Pac-Bio Sequencing of Porites lobata Flash Frozen Tissue Chunk

Trying Extraction Again With RNA Purelink Kit to Get RNA from 1 Porites asteroides Samples

Trying Extraction Again With RNA Purelink Kit to Get RNA from 3 Porites asteroides Samples Following Protocol from Federica

Using RNA Purelink Kit to Extract RNA from 3 Porites asteroides Samples Following Protocol from Federica

HMW DNA Extraction for Pac-Bio Sequencing of Pocillopora meandrina Flash Frozen Tissue Chunk

Using the Zymo Pico Methyl Seq Library Prep Kit for Two Final of Danielle’s Pocillopora DNA Samples for Whole Genome Bisulfite Sequencing

Using the Zymo Pico Methyl Seq Library Prep Kit for the 2nd Set of 16 of Danielle’s Pocillopora DNA Samples and Sample E7 Again for Whole Genome Bisulfite Sequencing

Using the Zymo Pico Methyl Seq Library Prep Kit for the 1st 16 of Danielle’s Pocillopora DNA Samples for Whole Genome Bisulfite Sequencing

Protocol For Using the Zymo Pico Methyl Seq Library Prep Kit

mtORF Amplification and Sanger Sequencing Prep for the Pocillopora Samples from the Mo’orea Connect Project

Protocol for mtORF Amplification and Sanger Sequencing for Determining Pocillopora Species

mtORF Amplification and Sanger Sequencing Prep for Danielle’s Pocillopora Samples

Bead Clean, Qubit Quantification, and Dilution and Aliquots for Sanger Sequencing of mtORF Amplifications

Testing Amplification of Danielle’s Pocillopora Samples and Reduced Cycle Number for mtORF Amplification

Resuspending RORF, Fatp6.1, POCHistoneF and POCHistoneR primers. Testing 5 samples from Mo’orea Connect project with mtORF PCR and gel.

Running Orthofinder for Montipora capitata and Pocillopora acuta peptide Fasta files

How to Add Sequence Files to the NCBI Sequence Read Archive

Specific Title Pertaining to Method and Samples Processed

Protocol Title: General for the Technique

Second Attempt At High Molecular Weight DNA Extraction of Porites asteroides with the Qiagen Genomic Tip for Intended Genome Sequencing

High Molecular Weight DNA Extraction of Porites asteroides with the Qiagen Genomic Tip for Intended Genome Sequencing

Using the Zymo Pico Methyl Seq Kit on the MBD enriched Eastern Oyster DNA from samples from Rebecca Stevick

Reduced Representation Bisulfite Sequencing Library Prep with the Zymo Research EZ DNA Methylation RRBS Library Prep Test Kit for Methylation Comparison

We have more free RNA Library Prep Kit Sequencing, using nutrient enriched and control treated eastern oysters (Crassostrea virginica) from Rebecca Stevick using the Zymo-Seq RiboFree Total RNA Library Prep Kit

Additional amplifications of already made libraries and two re-tries of the full library prep with samples from the previous post. Using the Zymo Pico Methyl Seq Kit for the purpose of comparing to RRBS preparations

Using the Zymo Pico Methyl Seq Kit on the MBD enriched 3 Pocillopora and 3 Montipora samples and non-enriched as whole genome bisulfite sequencing for the purpose of comparing them to RRBS preparations

Methyl-Binding Domain Enrichment of Samples for Methylation Comparison

Using the Zymo Pico Methyl Seq Kit on 3 Pocillopora and 3 Montipora samples for the purpose of whole genome bisulfate sequencing to compare to RRBS and MBD-BS preparations

Another free sequencing with the Zymo-Seq RiboFree Total RNA Library Prep Kit

Testing RNA Library Prep Kit on Porites Samples for Free Sequencing, using the Zymo-Seq RiboFree Total RNA Library Prep Kit

Extracting DNA and RNA from Porites astreoides corals for genome project to use the RNA for new Zymo Ribo-free RNASeq test kit

Testing Zymo Pico Methyl Seq Kit On Bisulfite Converted MBD Enriched Acropora Sperm Samples from Previous Post

Lightning Bisulfite Conversion of MBD Enriched Acropora Sperm Samples from Previous Post

Post bisulfite conversion samples from Previous Post hardly lost size at all, need to try again with a longer sonication.

Testing MethylMiner Kit on Two Samples to Prepare for Pico-Methyl Seq

General QSonica Protocol

Sonication Tests with Q800R3 Sonicator

Agilent Tape Station 4200

Mo’orea Connect Pocillopora (4 sites) EpiRAD ddRAD Library Prep Notebook and General Protocol

Using ddRADSeqTools, the Porites lutea genome, and the Pocillopora damicornis genome to simulate PstI and MspI restriction enzyme fragment distributions

12 Tests of Individual and Double Enzymes for Both Species

10 DNA only extractions from the first set of Porites and Pocillopora Corals from Mo’orea, 7 to try again, and 3 of Kevin’s Astrangia samples

One more 20 DNA only extractions from the first set of Porites and Pocillopora Corals from Mo’orea

And another(!) 20 DNA only extractions from Porites and Pocillopora Corals from Mo’orea

Another 20 DNA only extractions from Porites and Pocillopora Corals from Mo’orea

20 DNA only extractions from Porites and Pocillopora Corals from Mo’orea

18 DNA only extractions from Porites and Pocillopora Corals from Mo’orea

8 DNA only extractions from Porites and Pocillopora Corals from Mo’orea

I was not able to get good RNA at this time from the Zymo DNa/RNA kit. We are moving forward with trying a DNA only kit on the samples to save $, time, and reagents. This was also tried with two Mytilus californianus from the tide pool project that did not have good RNA with the other kit either.

Testing to get good RNA out of the Pocillopora and Porites Samples stored in RNA/RNA Shield from Mo’orea

DNA amounts for Pocillopora and Porites Mo’orea samples were really low in the previous extraction, and RNA quality for Porites was poor. We wanted to try bead homogenizing and incubating to see if un-digested proteins/sugars were inhibiting nucleic acid binding on the columns.

Previous DNA/RNA test extractions with the Montipora eggs and bundles from the biomineralization project showed some problems with reliably getting both DNA and RNA from the samples

Broad Range dsDNA, High Sensitivity dsDNA, Broad Range RNA, and High Sensitivity RNA

Agilent Tape Station 4200

this exercise is a modified from the Moore Laboratory of Zoology’s pipette exercise, which they modifed from somewhere else

Airbrushing and Concentrating

Whole mussels stored in -80, took out one plastic bag with 5 mussels

Using Zymo Duet DNA RNA Extraction Kit HERE

This protocol is for the Putnam, Prada, and Puritz Labs

Walk-though of Forking and Modifying this Notebook Site

All steps that can be done through the terminal instead of a GUI will be written for doing in the terminal because it is good practice to use the shell