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Analysis(7) • Processing(80) • Processing,(5) • ProjectSummaries(2) • Protocols(29) • Protocols,(12)

Analysis 7

Deep Dive WGBS Bioinformatics Test • February 17, 2025
Gene Expression Pipeline • March 12, 2024
Globus File Transfer Instructions • February 17, 2025
Moving Data from Unity to OSN Bucket • May 6, 2025
Point Judith Oyster RNAseq QC • January 12, 2023
Point Judith Oyster RNAseq Analysis • February 27, 2023
Running IGV Command Line on Unity • February 25, 2025

Processing 80

2022-10-03 ENCORE RNA and DNA Extractions • October 3, 2022
2022-10-05 ENCORE RNA and DNA Extractions • October 5, 2022
2022-10-17 ENCORE RNA and DNA Extractions • October 17, 2022
2022-10-19 ENCORE RNA and DNA Extractions • October 19, 2022
2022-10-21 ENCORE RNA and DNA Extractions • October 21, 2022
2022-10-24 ENCORE RNA and DNA Extractions • October 24, 2022
2022-10-26 ENCORE RNA and DNA Extractions • October 26, 2022
2022-10-27 Barott and Brown Pdam RNA and DNA Extractions • October 27, 2022
2022-10-31 ENCORE RNA and DNA Extractions • October 31, 2022
2022-11-02 Barott and Brown Pdam RNA and DNA Extractions • November 2, 2022
2022-11-08 Barott and Brown Pdam RNA and DNA Extractions • November 8, 2022
2022-11-11 Barott and Brown Pdam RNA and DNA Extractions • November 11, 2022
2022-11-18 Barott and Brown Pdam RNA and DNA Extractions • November 18, 2022
2022-12-02 Barott and Brown Pdam RNA Nanodrop • December 2, 2022
2022-12-02 Barott and Brown Pdam RNA Plate Prep • December 2, 2022
2023-01-13 ENCORE RNA and DNA Extractions • January 13, 2023
2023-01-18 ENCORE RNA and DNA Extractions • January 18, 2023
2023-01-23 E5 ACR Deep Dive RNA and DNA Extractions • January 23, 2023
2023-02-16 ENCORE RNA and DNA Extractions • February 16, 2023
2023-03-02 Pooling RNA Using Zymo Clean and Concentrate Kit for ENCORE Project • March 2, 2023
2023-03-15 E5 Site 1 Species ID (POC and POR) via PCR and Sanger Sequencing • March 15, 2023
2023-03-21 Paxgene Fixation, Stabilization, and Extraction Test • March 21, 2023
2023-04-06 ENCORE RNA and DNA Extractions • April 6, 2023
2023-04-11 E5 Sites 2 & 3 Species ID (POC and POR) via PCR and Sanger Sequencing • April 11, 2023
2023-04-11 Heron Island Pdam Species ID (mtORF confirmation) • April 11, 2023
2023-04-13 Paxgene Fixation, Stabilization, and Extraction Test • April 13, 2023
2023-04-18 ENCORE RNA and DNA Extractions • April 18, 2023
2023-04-21 ENCORE RNA and DNA Extractions • April 21, 2023
2023-04-25 ENCORE RNA and DNA Extractions • April 25, 2023
2023-04-27 ENCORE RNA and DNA Re-Extractions • April 27, 2023
2023-05-05 Pooling RNA Using Zymo Clean and Concentrate Kit for ENCORE Project • May 5, 2023
2023-05-08 ENCORE DLAB, MCAV, and MDEC TagSeq (RNA) Plate Prep • May 8, 2023
2024-08-01 E5 Time Series RNA and DNA Re-Extractions • August 1, 2024
2024-08-28 LCM Experiment Sample Prep • August 28, 2024
2024-09-08 LCM Experiment Test Extraction • September 8, 2024
2025-08-29 Time Series RNA Re-extractions • August 29, 2025
2025-09-05 Time Series RNA Re-extractions • September 5, 2025
2025-09-08 Time Series RNA Clean & Concentrate • September 8, 2025
2025-09-08 Time Series RNA-seq Plate Prep • September 8, 2025
2025-09-09 Time Series RNA Re-extractions • September 8, 2025
2026-06-10 Porites Time Series LCM Experiment • June 10, 2026
Continued Testing of Zymo Quick DNA/RNA Microprep Kit on LCM-d P. acuta and P. compressa • July 30, 2024
Extracting HMW DNA for P. tuahiniensis Genome • April 29, 2025
Extracting HMW DNA for P. tuahiniensis Genome with Qiagen Genomic Tip Protocol • July 16, 2025
Extracting RNA and DNA from Fixed P. acuta Sections (newly fixed 2/8/24) • February 15, 2024
Fixing Coral Tissues for LCM • April 29, 2024
Fixing Coral Tissues for Protocol Testing • August 30, 2023
Fixing Coral Tissues of Four Species to Compare Tissue Thickness • October 10, 2023
Fixing POC and POR Coral Tissues for LCM • July 3, 2024
Formalin-Fixed Paraffin Embedded Tissue Processing Protocol • August 16, 2025
Further Testing of Zymo Quick DNA/RNA Microprep Kit on LCM-d P. acuta and P. compressa • July 24, 2024
LCM Low Input RNA Library Prep • April 24, 2026
LCM Low Input RNA Library Prep • September 18, 2024
LCM Pico Methyl-Seq Library Prep • September 17, 2024
LCM Pilot Zymo Trio WGBS Library Prep Round 1 • December 6, 2024
LCM Pilot Zymo Trio WGBS Library Prep Round 2 • December 6, 2024
LCM Pilot Zymo Trio WGBS Library Prep Round 3 • December 15, 2024
LCM Pilot Zymo Trio WGBS Library Prep Testing • February 22, 2025
LCM Test 3, New Slide Prep Protocol • June 5, 2024
LCM Test 4, Porites and New Kits • July 18, 2024
Laser Capture Microdissection of Paxgene-Fixed Cryo-Embedded Tissue Protocol • April 25, 2026
Nuclei Isolation for Coral single nuclei RNA-seq • July 16, 2026
Paxgene-Fixed Cryo-Embedded Tissue H&E Staining Protocol • February 10, 2026
Paxgene-Fixed Cryo-Embedded Tissue Processing Protocol • September 10, 2025
Sending FF and PX corals for snSeq Trials • January 29, 2024
Suucessful? Testing of Charm Biotech DNA Extraction on LCM-d P. acuta • June 26, 2024
SwitchFree library prep • August 13, 2025
Testing Charm Biotech DNA Extraction on Cryosectioned P. comp and M. cap • February 9, 2024
Testing Charm Biotech DNA Extraction on Cryosectioned and LCM-d P. acuta • June 17, 2024
Testing Charm Biotech DNA Extraction on Cryosectioned and LCM-d P. acuta • May 14, 2024
Testing Charm Biotech RNA Extraction on Cryosectioned P. comp and M. cap • February 1, 2024
Testing Charm Biotech RNA Extraction on Cryosectioned and LCM-d P. acuta • May 13, 2024
Testing Charm Biotech RNA Extraction on Cryosectioned and LCM-d P. acuta • January 25, 2024
Testing Leica LDM7 Laser Capture Microdissection on P. acuta • October 16, 2023
Testing Zymo Quick DNA/RNA Microprep Kit on LCM-d P. acuta and P. compressa • July 19, 2024
Testing Zymo Quick RNA Microprep Kit on Cryosectioned and LCM-d P. acuta • June 13, 2024
Testing Zymo cfDNA DNA Extraction on Cryosectioned and LCM-d P. acuta • May 28, 2024
Testing of Charm Biotech DNA Extraction on LCM-d P. compressa • July 19, 2024
Testing of Charm Biotech DNA Extraction on LCM-d P. compressa and P. acuta • July 24, 2024
Troubleshooting Laser Capture Microdissection of *Porites compressa* • April 25, 2026

Processing, 5

2024-09-13 LCM Experiment Extractions • September 13, 2024
2026-02-13 Qiagen RNeasy Extraction Tests, PAXgene fixed tissue vs. Embedded tissue vs. Fresh Tissue • February 13, 2026
2026-02-19 Qiagen RNeasy Extraction Tests, PAXgene fixed tissue at various stages of decalcification • February 19, 2026
2026-03-10 Qiagen RNeasy Extraction Tests, Cryosectioned tissue optimization • March 10, 2026
2026-04-29 Zymo RNA Microprep Extraction Tests, Cryosectioned tissue • April 29, 2026

ProjectSummaries 2

2023-01-27 Project Summary Barott and Brown Pdam RNA and DNA Extractions • January 27, 2023
2023-05-09 Project Summary, 2022-2023 RNA and DNA Extractions for ENCORE MDEC Project • May 9, 2023

Protocols 29

2024-09-13 LCM Experiment Extractions • September 13, 2024
2026-02-13 Qiagen RNeasy Extraction Tests, PAXgene fixed tissue vs. Embedded tissue vs. Fresh Tissue • February 13, 2026
2026-02-19 Qiagen RNeasy Extraction Tests, PAXgene fixed tissue at various stages of decalcification • February 19, 2026
2026-03-10 Qiagen RNeasy Extraction Tests, Cryosectioned tissue optimization • March 10, 2026
2026-04-29 Zymo RNA Microprep Extraction Tests, Cryosectioned tissue • April 29, 2026
2026-05-08 LCM RNA Extraction Protocol • May 8, 2026
Adult Coral RNA and DNA Extraction using the Zymo Quick-DNA/RNA™ Miniprep Plus Kit • October 3, 2022
Charm Biotech Just-a-Tube ™ Laser Captured Microdissection (LCM) Sample Genomic DNA Purification Kit • January 31, 2024
Charm Biotech Just-a-Tube ™ Laser Captured Microdissection (LCM) Sample Total RNA/MicroRNA Purification Kit • January 25, 2024
LCM Zymo Trio WGBS Library Prep • December 3, 2024
PCR Protocol • March 14, 2023
PPP Lab Agarose Gel Protocol • October 2, 2022
PPP Lab RNA Tape Station Protocol • October 2, 2022
Protocol for Cryoembedding Tissues in OCT Media for Cryosectioning (for FISH, Immunofluorescence, and LCM) • August 22, 2023
Protocol for Cryosectioning Tissues (for FISH, Immunofluorescence, and LCM) • August 31, 2023
Protocol for Fixing Coral Tissues with PAXgene Tissue Fixative followed by EDTA Decalcification • August 21, 2023
Putnam Lab Physiology Airbrushing Protocol • June 19, 2023
Putnam Lab Physiology Ash Free Dry Weight Protocol • June 23, 2023
Putnam Lab Physiology Chlorophyll Protocol • June 19, 2023
Putnam Lab Physiology Soluble Protein Protocol • June 22, 2023
Putnam Lab Physiology Surface Area by Wax Dipping • June 30, 2023
Putnam Lab Physiology Symbiont Density Protocol • June 19, 2023
Qiagen AllPrep DNA/RNA FFPE Kit Protocol • January 25, 2024
RNA Nanodrop Purity Check and Quantification Protocol • October 2, 2022
Testing NEBNext Low Input RNA Library Prep • August 1, 2024
Testing PAXgene, PFA, (and Z-fix) for Immunofluorescence, FISH + LCM preps and sectioning • August 14, 2023
Testing Pico Methyl-Seq Library Prep • August 27, 2024
Using renv for Reproducible Environments in R • April 30, 2024
dsDNA and RNA Qubit Quantification Protocol • October 2, 2022

Protocols, 12

Extracting HMW DNA for P. tuahiniensis Genome • April 29, 2025
Extracting HMW DNA for P. tuahiniensis Genome with Qiagen Genomic Tip Protocol • July 16, 2025
Formalin-Fixed Paraffin Embedded Tissue Processing Protocol • August 16, 2025
LCM Low Input RNA Library Prep • April 24, 2026
LCM Low Input RNA Library Prep • September 18, 2024
LCM Pico Methyl-Seq Library Prep • September 17, 2024
Laser Capture Microdissection of Paxgene-Fixed Cryo-Embedded Tissue Protocol • April 25, 2026
Nuclei Isolation for Coral single nuclei RNA-seq • July 16, 2026
Paxgene-Fixed Cryo-Embedded Tissue H&E Staining Protocol • February 10, 2026
Paxgene-Fixed Cryo-Embedded Tissue Processing Protocol • September 10, 2025
SwitchFree library prep • August 13, 2025
Troubleshooting Laser Capture Microdissection of *Porites compressa* • April 25, 2026