• Extracting RNA from PAXgene fixed tissue at various stages of decalcification
  • Timeline
  • Protocol: Qiagen RNeasy Kit
  • 2/19/26: Pre-decalc samples, testing ProK digestion vs. no digestion
  • 2/21/26: First 24 and 48 hours of decalcification results
  • 2/22/26: First 24 and 48 hours of decalcification results, re-extraction of POR + MON
    • Total count of extractions used from this kit (50 preps):
  • 3/2/26: 72 hours decalcification extraction
• 2/22/26: All final blocks embedded, details in google sheet and notebook
• Embedded blocks were sectioned 2/26/26 and 2/27/26:
• 3/3/26: Tissue scrolls extraction
• YAY! We have tissue scrolls with RINs at 6.9 for POC and > 7 for POR. The non-sucrose slides still don’t look like the morphology we want, but this is major progress.

Extracting RNA from PAXgene fixed tissue, PAXgene fixed & Embedded Tissue, and Fresh Tissue

Paxgene-Fixed Cryo-Embedded Tissue Processing Protocol

Prep and submit RNA for TimeSeries Project, September 8-9, 2025 (to be sent to Genohub Sequencer in OK)

RNA Re-extractions for Time Series Project, September 9, 2025

RNA Re-extractions for Time Series Project, September 8, 2025

RNA Re-extractions for Time Series Project, September 5, 2025

RNA Re-extractions for Time Series Project, August 29, 2025

Formalin-Fixed Paraffin Embedded Tissue Processing Protocol

“TagSeq” Zymo Switch-Free RNA Library Prep Test/Protocol

Extracting HMW DNA for P. tuahiniensis Genome, sample POC-222

Transferring Data to OSN Storage Bucket

Extracting HMW DNA for P. tuahiniensis Genome, sample POC-222

How to use IGV on Unity

LCM Zymo Trio WGBS Library Prep

How to move files from Andromeda to Unity

Deep Dive WGBS Bioinformatics Test

LCM Zymo Trio WGBS Library Prep

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 Pico Methyl-Seq Library Prep

Extracting RNA and DNA from LCM-d Pocillopora for LCM Experiment

Extracting RNA and DNA from LCM-d Pocillopora for LCM Experiment

Fixing and decalcifying Pocillopora for LCM Experiment

Testing NEBNext Low Input RNA Library Prep

Testing NEBNext Low Input RNA Library Prep

E5 Time Series RNA and DNA Re-Extractions, August 1, 2024

Continued Testing of Zymo Quick-DNA/RNA Microprep Kit on 7/18 LCM Samples

Further Testing of Zymo Quick-DNA/RNA Microprep Kit on 7/18 LCM Samples

Testing Charm DNA Kit on 7/18 LCM Samples, Second Try

Testing Zymo Quick-DNA/RNA Microprep Kit on 7/18 LCM Samples

Testing Charm DNA Kit on 7/18 LCM Samples

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 and decalcifying Pocillopora and Porites tissue for LCM, to further improve sectioning and extractions

Testing Charm DNA Kit on LCM Samples

Testing Charm DNA Kit on LCM Samples

Testing Zymo Quick-RNA Microprep Kit on LCM Samples

Fixing and decalcifying Pocillopora tissue for LCM, second test before summer experiments

Testing Zymo cfDNA Kit on LCM Samples

Testing Charm DNA Kit on LCM Samples

Testing Charm RNA Kit on LCM Samples

Using renv for Reproducible Environments in R

Fixing and decalcifying Pocillopora tissue for LCM, second test before summer experiments

RNA-seq Data Processing Pipeline

Extracting RNA and DNA from Fixed P. acuta Sections (newly fixed 2/8/24)

Testing Charm DNA Kit on P. comp and M. cap

Testing Charm Kit on P. comp and M. cap

Goal: to extract high-quality gDNA from PAXgene-fixed cryosectioned tissue.

Flash freezing fragments from three species from CBLS wetlab

Testing Charm Kit on P. acuta

Goal: to extract high-quality gDNA and total RNA from PAXgene-fixed cryosectioned tissue.

Goal: to extract high-quality RNA from PAXgene-fixed cryosectioned tissue.

Testing Laser Capture Microdissection

Fixing and decalcifying fragments from four species from CBLS wetlab

Protocol for Cryosectioning PAXgene-fixed Tissues (for FISH, Immunofluorescence, and LCM)

Fixing and decalcifying 16 branches of Pocillopora tissue for testing protocols

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

Immunofluorescence and FISH Preparation: Testing PAXgene, PFA, (and Z-fix) for FISH + LCM preps and cryosectioning

Wax Dipping: Coral surface area measurments using a paraffin wax bath

Ash Free Dry Weight: Measuring Biomass from Coral Tissue Homogenate

Soluble Protein Protocol from Coral Tissue Homogenate, Separated into Host and Holobiont Fractions

Symbiodiniaceae Cell Density Counting Protocol from Coral Tissue Homogenate

Chlorophyll-a Extraction and Quantification from Coral Tissue Homogenate

Airbrushing Coral Homogenate for Physiological Analyses

Project Summary: 2022-2023 RNA and DNA Extractions for ENCORE MDEC Project

Prep and submit RNA for ENCORE Project, May 8, 2023 (to be sent to UT Austin sometime this summer)

Concentrating Low-Quantity ENCORE RNA and Pooling Re-extractions Using Zymo Clean and Concentrate Kit for ENCORE Project, May 5, 2023

RNA and DNA Re-Extractions for ENCORE Project, April 27, 2023

RNA and DNA Extractions for ENCORE Project, April 25, 2023

RNA and DNA Extractions for ENCORE Project, April 21, 2023

RNA and DNA Extractions for ENCORE Project, April 18, 2023

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

E5 Species ID (POC and POR) via PCR and Sanger Sequencing: Sites 2 and 3

Heron Island Pdam Species ID (mtORF confirmation) of samples that were originally not able to be amplified via PCR and Sanger Sequencing

RNA and DNA Extractions for ENCORE Project, April 6, 2023

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

E5 Species ID (POC and POR) via PCR and Sanger Sequencing

PCR Protocol for POC and POR Species ID (Can be modified for other primers)

Pooling RNA Using Zymo Clean and Concentrate Kit for ENCORE Project, March 2, 2023

Point Judith Oyster RNAseq Analysis

Point Judith Oyster RNAseq Initial QC : https://zdellaert.github.io/ZD_Putnam_Lab_Notebook/Point-Judith-RNAseq-QC/

RNA and DNA Extractions for ENCORE Project, February 16, 2023

Project Summary: 2022 RNA and DNA Extractions for Brown/Barott Pdam Project

RNA and DNA Extractions for E5 ACR Deep Dive Project, January 23, 2023

RNA and DNA Extractions for ENCORE Project, January 18, 2023

RNA and DNA Extractions for ENCORE Project, January 13, 2023

Point Judith Oyster RNAseq Initial QC

Prep and submit RNA for Brown/Barott Pdam Project, December 2, 2022

QC of RNA for Brown/Barott Pdam Project, December 2, 2022

RNA and DNA Extractions for Brown/Barott Pdam Project, November 18, 2022

RNA and DNA Extractions for Brown/Barott Pdam Project, November 11, 2022

RNA and DNA Extractions for Brown/Barott Pdam Project, November 8, 2022

RNA and DNA Extractions for Brown/Barott Pdam Project, November 2, 2022

RNA and DNA Extractions for ENCORE Project, October 31, 2022

RNA and DNA Extractions for Brown/Barott Pdam Project, October 27, 2022

RNA and DNA Extractions for ENCORE Project, October 26, 2022

RNA and DNA Extractions for ENCORE Project, October 24, 2022

RNA and DNA Extractions for ENCORE Project, October 21, 2022

RNA and DNA Extractions for ENCORE Project, October 19, 2022

RNA and DNA Extractions for ENCORE Project, October 17, 2022

RNA and DNA Extractions for ENCORE Project, October 05, 2022

RNA and DNA Extractions for ENCORE Project, October 03, 2022

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.

Agilent Tape Station 4200

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

NanoDrop for RNA Protocol

This protocol was written by Maggie Schedl for the Putnam, Prada, and Puritz labs