Extracting HMW DNA for P. tuahiniensis Genome
Extracting HMW DNA for P. tuahiniensis Genome, sample POC-222
Running IGV Command Line on Unity
How to use IGV on Unity
LCM Pilot Zymo Trio WGBS Library Prep Testing
LCM Zymo Trio WGBS Library Prep
Globus File Transfer Instructions
How to move files from Andromeda to Unity
Deep Dive WGBS Bioinformatics Test
Deep Dive WGBS Bioinformatics Test
LCM Pilot Zymo Trio WGBS Library Prep Round 3
LCM Zymo Trio WGBS Library Prep
LCM Pilot Zymo Trio WGBS Library Prep Round 2
LCM Zymo Trio WGBS Library Prep
LCM Pilot Zymo Trio WGBS Library Prep Round 1
LCM Zymo Trio WGBS Library Prep
LCM Zymo Trio WGBS Library Prep
LCM Zymo Trio WGBS Library Prep
LCM Low Input RNA Library Prep
LCM Low Input RNA Library Prep
LCM Pico Methyl-Seq Library Prep
LCM Pico Methyl-Seq Library Prep
2024-09-13 LCM Experiment Extractions
Extracting RNA and DNA from LCM-d Pocillopora for LCM Experiment
2024-09-08 LCM Experiment Test Extraction
Extracting RNA and DNA from LCM-d Pocillopora for LCM Experiment
2024-08-28 LCM Experiment Sample Prep
Fixing and decalcifying Pocillopora for LCM Experiment
Testing Pico Methyl-Seq Library Prep
Testing NEBNext Low Input RNA Library Prep
Testing NEBNext Low Input RNA Library Prep
Testing NEBNext Low Input RNA Library Prep
2024-08-01 E5 Time Series RNA and DNA Re-Extractions
E5 Time Series RNA and DNA Re-Extractions, August 1, 2024
Continued Testing of Zymo Quick DNA/RNA Microprep Kit on LCM-d P. acuta and P. compressa
Continued Testing of Zymo Quick-DNA/RNA Microprep Kit on 7/18 LCM Samples
Further Testing of Zymo Quick DNA/RNA Microprep Kit on LCM-d P. acuta and P. compressa
Further Testing of Zymo Quick-DNA/RNA Microprep Kit on 7/18 LCM Samples
Testing of Charm Biotech DNA Extraction on LCM-d P. compressa and P. acuta
Testing Charm DNA Kit on 7/18 LCM Samples, Second Try
Testing Zymo Quick DNA/RNA Microprep Kit on LCM-d P. acuta and P. compressa
Testing Zymo Quick-DNA/RNA Microprep Kit on 7/18 LCM Samples
Testing of Charm Biotech DNA Extraction on LCM-d P. compressa
Testing Charm DNA Kit on 7/18 LCM Samples
LCM Test 4, Porites and New Kits
Sectioning and performing LCM on the POC and POR branches that were prepared on 7/10/24, using the same steps outlined in this early June post
Fixing POC and POR Coral Tissues for LCM
Fixing and decalcifying Pocillopora and Porites tissue for LCM, to further improve sectioning and extractions
Suucessful? Testing of Charm Biotech DNA Extraction on LCM-d P. acuta
Testing Charm DNA Kit on LCM Samples
Testing Charm Biotech DNA Extraction on Cryosectioned and LCM-d P. acuta
Testing Charm DNA Kit on LCM Samples
Testing Zymo Quick RNA Microprep Kit on Cryosectioned and LCM-d P. acuta
Testing Zymo Quick-RNA Microprep Kit on LCM Samples
LCM Test 3, New Slide Prep Protocol
Fixing and decalcifying Pocillopora tissue for LCM, second test before summer experiments
Testing Zymo cfDNA DNA Extraction on Cryosectioned and LCM-d P. acuta
Testing Zymo cfDNA Kit on LCM Samples
Testing Charm Biotech DNA Extraction on Cryosectioned and LCM-d P. acuta
Testing Charm DNA Kit on LCM Samples
Testing Charm Biotech RNA Extraction on Cryosectioned and LCM-d P. acuta
Testing Charm RNA Kit on LCM Samples
Using renv for Reproducible Environments in R
Using renv for Reproducible Environments in R
Fixing Coral Tissues for LCM
Fixing and decalcifying Pocillopora tissue for LCM, second test before summer experiments
Gene Expression Pipeline
RNA-seq Data Processing Pipeline
Extracting RNA and DNA from Fixed P. acuta Sections (newly fixed 2/8/24)
Extracting RNA and DNA from Fixed P. acuta Sections (newly fixed 2/8/24)
Testing Charm Biotech DNA Extraction on Cryosectioned P. comp and M. cap
Testing Charm DNA Kit on P. comp and M. cap
Testing Charm Biotech RNA Extraction on Cryosectioned P. comp and M. cap
Testing Charm Kit on P. comp and M. cap
Charm Biotech Just-a-Tube ™ Laser Captured Microdissection (LCM) Sample Genomic DNA Purification Kit
Goal: to extract high-quality gDNA from PAXgene-fixed cryosectioned tissue.
Sending FF and PX corals for snSeq Trials
Flash freezing fragments from three species from CBLS wetlab
Testing Charm Biotech RNA Extraction on Cryosectioned and LCM-d P. acuta
Testing Charm Kit on P. acuta
Qiagen AllPrep DNA/RNA FFPE Kit Protocol
Goal: to extract high-quality gDNA and total RNA from PAXgene-fixed cryosectioned tissue.
Charm Biotech Just-a-Tube ™ Laser Captured Microdissection (LCM) Sample Total RNA/MicroRNA Purification Kit
Goal: to extract high-quality RNA from PAXgene-fixed cryosectioned tissue.
Testing Leica LDM7 Laser Capture Microdissection on P. acuta
Testing Laser Capture Microdissection
Fixing Coral Tissues of Four Species to Compare Tissue Thickness
Fixing and decalcifying fragments from four species from CBLS wetlab
Protocol for Cryosectioning Tissues (for FISH, Immunofluorescence, and LCM)
Protocol for Cryosectioning PAXgene-fixed Tissues (for FISH, Immunofluorescence, and LCM)
Fixing Coral Tissues for Protocol Testing
Fixing and decalcifying 16 branches of Pocillopora tissue for testing protocols
Protocol for Cryoembedding Tissues in OCT Media for Cryosectioning (for FISH, Immunofluorescence, and LCM)
Protocol for Cryoembedding PAXgene-fixed Tissues in OCT Media for Cryosectioning (for FISH, Immunofluorescence, and LCM)
Protocol for Fixing Coral Tissues with PAXgene Tissue Fixative followed by EDTA Decalcification
Protocol for Fixing Coral Tissues with PAXgene Tissue Fixative followed by EDTA Decalcification
Testing PAXgene, PFA, (and Z-fix) for Immunofluorescence, FISH + LCM preps and sectioning
Immunofluorescence and FISH Preparation: Testing PAXgene, PFA, (and Z-fix) for FISH + LCM preps and cryosectioning
Putnam Lab Physiology Surface Area by Wax Dipping
Wax Dipping: Coral surface area measurments using a paraffin wax bath
Putnam Lab Physiology Ash Free Dry Weight Protocol
Ash Free Dry Weight: Measuring Biomass from Coral Tissue Homogenate
Putnam Lab Physiology Soluble Protein Protocol
Soluble Protein Protocol from Coral Tissue Homogenate, Separated into Host and Holobiont Fractions
Putnam Lab Physiology Symbiont Density Protocol
Symbiodiniaceae Cell Density Counting Protocol from Coral Tissue Homogenate
Putnam Lab Physiology Chlorophyll Protocol
Chlorophyll-a Extraction and Quantification from Coral Tissue Homogenate
Putnam Lab Physiology Airbrushing Protocol
Airbrushing Coral Homogenate for Physiological Analyses
2023-05-09 Project Summary, 2022-2023 RNA and DNA Extractions for ENCORE MDEC Project
Project Summary: 2022-2023 RNA and DNA Extractions for ENCORE MDEC Project
2023-05-08 ENCORE DLAB, MCAV, and MDEC TagSeq (RNA) Plate Prep
Prep and submit RNA for ENCORE Project, May 8, 2023 (to be sent to UT Austin sometime this summer)
2023-05-05 Pooling RNA Using Zymo Clean and Concentrate Kit for ENCORE Project
Concentrating Low-Quantity ENCORE RNA and Pooling Re-extractions Using Zymo Clean and Concentrate Kit for ENCORE Project, May 5, 2023
2023-04-27 ENCORE RNA and DNA Re-Extractions
RNA and DNA Re-Extractions for ENCORE Project, April 27, 2023
2023-04-25 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, April 25, 2023
2023-04-21 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, April 21, 2023
2023-04-18 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, April 18, 2023
2023-04-13 Paxgene Fixation, Stabilization, and Extraction Test
Testing Paxgene Fixative, PAXgene Tissue Stabilizer, Sectioning, Decalcification, and Extraction of DNA/RNA using Zymo Quick DNA/RNA Protocol from Stabilized Samples (Time Course), April 13, 2023
2023-04-11 E5 Sites 2 & 3 Species ID (POC and POR) via PCR and Sanger Sequencing
E5 Species ID (POC and POR) via PCR and Sanger Sequencing: Sites 2 and 3
2023-04-11 Heron Island Pdam Species ID (mtORF confirmation)
Heron Island Pdam Species ID (mtORF confirmation) of samples that were originally not able to be amplified via PCR and Sanger Sequencing
2023-04-06 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, April 6, 2023
2023-03-21 Paxgene Fixation, Stabilization, and Extraction Test
Testing Paxgene Fixative, PAXgene Tissue Stabilizer, and Extraction of DNA/RNA using Zymo Quick DNA/RNA Protocol from Stabilized Samples (Time Course), March 21, 2023
2023-03-15 E5 Site 1 Species ID (POC and POR) via PCR and Sanger Sequencing
E5 Species ID (POC and POR) via PCR and Sanger Sequencing
PCR Protocol
PCR Protocol for POC and POR Species ID (Can be modified for other primers)
2023-03-02 Pooling RNA Using Zymo Clean and Concentrate Kit for ENCORE Project
Pooling RNA Using Zymo Clean and Concentrate Kit for ENCORE Project, March 2, 2023
Point Judith Oyster RNAseq Analysis
Point Judith Oyster RNAseq Analysis
Point Judith Oyster RNAseq Initial QC : https://zdellaert.github.io/ZD_Putnam_Lab_Notebook/Point-Judith-RNAseq-QC/
2023-02-16 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, February 16, 2023
2023-01-27 Project Summary Barott and Brown Pdam RNA and DNA Extractions
Project Summary: 2022 RNA and DNA Extractions for Brown/Barott Pdam Project
2023-01-23 E5 ACR Deep Dive RNA and DNA Extractions
RNA and DNA Extractions for E5 ACR Deep Dive Project, January 23, 2023
2023-01-18 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, January 18, 2023
2023-01-13 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, January 13, 2023
Point Judith Oyster RNAseq QC
Point Judith Oyster RNAseq Initial QC
2022-12-02 Barott and Brown Pdam RNA Plate Prep
Prep and submit RNA for Brown/Barott Pdam Project, December 2, 2022
2022-12-02 Barott and Brown Pdam RNA Nanodrop
QC of RNA for Brown/Barott Pdam Project, December 2, 2022
2022-11-18 Barott and Brown Pdam RNA and DNA Extractions
RNA and DNA Extractions for Brown/Barott Pdam Project, November 18, 2022
2022-11-11 Barott and Brown Pdam RNA and DNA Extractions
RNA and DNA Extractions for Brown/Barott Pdam Project, November 11, 2022
2022-11-08 Barott and Brown Pdam RNA and DNA Extractions
RNA and DNA Extractions for Brown/Barott Pdam Project, November 8, 2022
2022-11-02 Barott and Brown Pdam RNA and DNA Extractions
RNA and DNA Extractions for Brown/Barott Pdam Project, November 2, 2022
2022-10-31 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, October 31, 2022
2022-10-27 Barott and Brown Pdam RNA and DNA Extractions
RNA and DNA Extractions for Brown/Barott Pdam Project, October 27, 2022
2022-10-26 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, October 26, 2022
2022-10-24 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, October 24, 2022
2022-10-21 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, October 21, 2022
2022-10-19 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, October 19, 2022
2022-10-17 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, October 17, 2022
2022-10-05 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, October 05, 2022
2022-10-03 ENCORE RNA and DNA Extractions
RNA and DNA Extractions for ENCORE Project, October 03, 2022
Adult Coral RNA and DNA Extraction using the Zymo Quick-DNA/RNA™ Miniprep Plus Kit
This protocol is based off of the base Zymo protocol, which was adjusted for Putnam Lab needs by Emma L. Strand, Dr. Kevin H. Wong (and here), and Erin E. Chille. Kristina Terpis (Porites sp. example) modified this protocol for coral clippings stored in 1mL of Zymo DNA/RNA shield and kept at -80 ºC.