Assessing PolyIC and hardening Effort A project oysters at Sequim Bay
Today I took images and assessed oysters at Sequim Bay from the PolyIC project and Effort A of our hardening efforts.
October 2025 Goals
October 2025 goals and daily notebook entries.
All Projects To Do List
This post lists all my ongoing projects and to-do list.
Writing updates
I have listed active manuscripts below and their status along with my writing goals!
Download and QC of Moorea 2023 RNAseq files with NCBI upload
Today I downloaded RNAseq files from GenoHub for the 2023 Moorea Symbiotic Exchange project.
Growth analysis of outplants Manchester
This post details initial growth analysis of our field deployments for our Manchester hardening experiment at the Manchester NOAA station.
September 2025 Goals
September goals and daily notebook entries.
Resazurin family screening with Taylor Shelfish with individual size normalization
This post details analysis of Taylor Shellfish family resazurin screening using individual size normalization.
Assessing field outplants at Manchester
This post details assessments on our field deployments for our Manchester hardening experiment at the Manchester NOAA station.
New Guava Muse instrument set up and testing
This post details set up and testing of the replacement Cytek Guava Muse instrument.
Resazurin family screening with Taylor Shelfish with mean family size normalization
This post details analysis of Taylor Shellfish family resazurin screening.
Goose Point Oyster Summer Year 2 Assessment Analysis
This post summarizes size analysis of oyster outplants at the Goose Point site up to the 20250825 sampling time point.
Resazurin family screening with Taylor Shelfish
We are conducting resazurin oyster family screenings with seed provided by Taylor Shellfish.
Coral Metabolomics Extraction Log for Moorea 2023 Project
This post details metaboloimcs extractions for the 2023 Moorea Symbiotic Exchange project.
Coral Metabolomics Extraction Protocol for 2023 Moorea Project
This post details metaboloimcs extraction protocols for the 2023 Moorea Symbiotic Exchange project, which contains both larval and recruit samples.
VIMS Ploidy Resazurin Trials - Round 2
This post details resazurin trials at VIMS between diploids and triploids. Experiments were conducted at VIMS and I analyzed the data. This is the second round of trials that included blanks and will be used to track individual performance through time.
Goose Point Outplant Assessments 25 August 2025
Today we assessed Goose Point seed outplants near Willapa Bay, WA.
August 2025 Goals
August goals and daily notebook entries.
Baywater 10K Seed Outplant Survival
I did a quick assessment of survival of 10K seed from our assessments yesterday. Here are the results.
Baywater Outplant Assessments and Deployments 20 August 2025
Today we assessed 10K seed outplants at Baywater Shellfish in the Hood Canal, WA and outplanted the remaining PolyIC seed for future assessments.
VIMS Ploidy Resazurin Trials
This post details resazurin trials at VIMS between diploids and triploids. Experiments were conducted at VIMS and I analyzed the data.
Oyster oxygen-resazurin correlations Round 2
This post details activities of 1) oxygen measurements of 87 oysters to calculate respiration rates via oxygen evolution, 2) resazurin measurements of those same oysters, and 3) correlation of oxygen and resazurin measurements to test for a relationship between the two.
Locating outplants at Baywater
Today Steven, Valentina, and I searched the field at Baywater (Thorndyke Bay, Hood Canal) to find our outplants from this past winter for the 10K seed project.
Oxygen measurements for oyster oxgen-resazurin correlations
This post details activities of oxygen measurements of ~70 oysters to calculate respiration rates via oxygen evolution to correlate to resazurin responses measured earlier this week.
Resazurin measurements for oyster oxgen correlations
This post details activities of resazurin measurements of 80 oysters to calculate resazurin response to correlate to oxygen measurements later this week.
July 2025 Goals
July goals and daily notebook entries.
RNA Extraction Log for 2023 Moorea Project
This post details RNA extractions for the 2023 Moorea Symbiotic Exchange project, which contains both larval and recruit samples.
Coral RNA Extraction Protocol for 2023 Moorea Project
This post details RNA extraction protocols for the 2023 Moorea Symbiotic Exchange project, which contains both larval and recruit samples.
Checking field outplants at Manchester
This post details checking on our field deployments for our Manchester hardening experiment at the Manchester NOAA station.
Outplanting PolyIC project oysters at Sequim Bay
Today Steven and I outplanted oysters at Sequim Bay from the PolyIC project.
VIMS Resazurin Trials Day 4
This post details resazurin trials at VIMS from Day 4. Today we ran full family trials with temperature exposure in the same way we ran trials the last two days.
VIMS Resazurin Trials Day 3
This post details resazurin trials at VIMS from Day 3. Today we ran full family trials with temperature exposure in the same way we ran trials yesterday.
VIMS Resazurin Trials Day 2
This post details resazurin trials at VIMS from Day 2. Today we ran full family trials with temperature exposure.
VIMS Resazurin Trials Day 1
This post details resazurin trials at VIMS. Today, we conducted temperature testing and prepared supplies for full trials. We used data from today to make decisions about trial conditions tomorrow.
Preparing PolyIC project outplants at Point Whitney
Today I went to Point Whitney to prepare PolyIC project oysters for field outplants.
June 2025 Goals
June goals and daily notebook entries.
Resazurin testing of open and closed oysters
This post details activities of a resazurin trial to measure fluorescence in oysters and monitor whether they were open or closed at the time of measurement.
Field outplants at Manchester
This post details launching field deployments for our Manchester hardening experiment at the Manchester NOAA station.
USDA Families Resazurin Trials Complete Results
This post details the results from all completed resazurin trials testing individual oyster stress responses. In these trials we compared metabolic rates of oysters as they go from control to high temperature.
Guava Muse status
We have a Muse Guava flow cytometer in our lab and our undergraduate researcher, Aakriti, has been managing the instrument and is working to test out kits and protocols.
Goose Point Oyster Spring Assessment Analysis
This post summarizes size analysis of oyster outplants at the Goose Point site.
Sequim Bay Oyster Spring Assessment
This post summarizes size analysis of oyster outplants at the Sequim Bay site.
Coral Cell Count Protocol
This post details symbiont cell counting protocol for the 2023 Montipora capitata larval samples.
USDA Families Resazurin Trials 3 June 2025
This post details activities of a resazurin trial from 3 June 2025 and preliminary data analysis. In this trial we are comparing metabolic rates of oysters as they go from control to high temperature.
Launching experiment at Manchester and maintaining stocks at Point Whitney
This post details launching a new experiment at the Manchester NOAA station and conducting maintenance of stocks at the Point Whitney hatchery.
May 2025 Goals
May goals and daily notebook entries.
Sequim Bay Oyster Spring Assessment
This post summarizes field activities to assess growth and survival of oyster outplants at Sequim Bay in Sequim, WA.
Coral Metabolomics Extraction and Preparation Protocol for 2023 Moorea Project
This post details protocols for metabolite extraction and preparation for analysis in the 2023 Moorea Symbiotic Nutritional Exchange project.
USDA Families Resazurin Trials 20 May 2025
This post details activities of a resazurin trial from 20 May 2025 and preliminary data analysis. In this trial we are comparing metabolic rates of oysters as they go from control to high temperature.
Goose Point Oyster Spring Assessment
This post summarizes field activities to assess growth and survival of oyster outplants at Goose Point Oysters in South Bend, WA.
E5 metabolomics preliminary analysis
This post details preliminary data analysis of metabolomic reponses of corals in the E5 timeseries project.
E5 timeseries energy state exploratory analysis Part 2
This post details preliminary data analysis to identify lipidomic and metabolomic indicators of coral energetic state for the E5 Modeler Team.
Westcott Oyster Spring Assessment
This post summarizes field activities to assess growth and survival of oyster outplants at Westcott Shellfish on San Juan Island.
USDA Families Resazurin Trials 13 May 2025
This post details activities of a resazurin trial from 13 May 2025 and preliminary data analysis. In this trial we are comparing metabolic rates of oysters as they go from control to high temperature.
Finishing growth analysis for the lifestage carry over project
This post details growth analyses for the Lifestage Carry Over project in the Roberts Lab.
Goose Point Growth Analysis for December Oyster Data
This post summarizes revised growth analysis for oyster outplants at the Goose Point site from December 2024 measurements.
USDA Families Resazurin Trials 6 May 2025
This post details activities of a resazurin trial from 6 May 2025 and preliminary data analysis. In this trial we are comparing metabolic rates of oysters as they go from control to high temperature.
Oyster Size Analysis Protocol - Written by Noah Krebs
This post details Noah Kreb’s ImageJ analysis to measure oyster size and counts originally posted in the notebook post here.
Resazurin Metabolic Assays Protocol for Individual Stress Testing
This post details the working protocol for test of individual oyster response to stress using the resazurin metabolic assay. This protocol is used to measure change in metabolism from ambient to high temperature in individual seed.
E5 timeseries energy state exploratory analysis Part 1
This post details our first attempt at an exploratory analysis to examine gene expression indicators of energetic state. We examined expression of genes involved in key metabolic pathways of energy metabolism and storage across time in our E5 time series molecular project.
April 2025 Goals
April goals and daily notebook entries.
Resazurin Metabolic Assays Protocol for Steven's VIMS trip
This post details the working protocol for test of individual oyster response to stress using the resazurin metabolic assay. This protocol is meant for demonstration purposes only.
Poly IC Resazurin Trials 20 March 2025
This post details results from resazurin trials of PolyIC seed from 20 March 2025 run at control (20°C) and high (38°C) temperatures. This is the last resazurin run for these samples.
ITS2 amplicon sequencing preparation protocol
This protocol details sample preparation for next-generation sequencing of ITS2 amplicons for identification of Symbiodiniaceae in reef-building coral samples.
Revising RDA plots for E5 physiology manuscript
Today I revised our redundancy analysis (RDA) plots to better visualize the relationship between physiological metrics and environmental variables.
Data transfer from Andromeda to Unity and Hyak
Today I transferred and backed up data from Andromeda (URI server) to Unity and UW Hyak servers.
Sample transport to UW for Moorea 2023 project
Today I prepared samples to transport to UW for RNA and metabolomics processing.
March 2025 Goals
March goals and daily notebook entries.
Tank cleaning and new tanks in FTR
Today I cleaned the tanks in FTR and Jon moved in new tanks to the tank room.
Poly IC Resazurin Trials 18 March 2025
This post details results from resazurin trials of PolyIC seed from 18 March 2025 run at control (20°C) and high (42°C) temperatures. This is a continuation of trials I ran earlier this week.
E5 molecular timeseries lipidomics preliminary analysis
This post details analysis of lipidomic samples for the E5 timeseries molecular project.
Poly IC Resazurin Trials 13 March 2025
This post details results from resazurin trials of PolyIC seed from 13 March 2025 run at control (20°C) and high (36°C) temperatures. This is a continuation of trials I ran earlier this week.
COTS Project Bioinformatic Analysis
This post details scripts for bioinformatics processing of COTS Project RNAseq data.
Poly IC Resazurin Trials 10 March 2025
This post details results from resazurin trials of PolyIC seed from 10 March 2025 run at control (20°C) and high (40°C) temperatures.
PolyIC Seed RNAseq Planning
This post details plans for an RNAseq experiment for the PolyIC project.
Testing resazurin readings on FLx800 instrument
This post details my tests and set up for resazurin readings on the FLx800 instrument in the MERLAB.
Analysis of DNA sequences for species identification in the Moorea 2023 project
This post details analysis of DNA sequences for species identification of Pocillopora, Porites, and Acropora samples from the Moorea 2023 project.
February 2025 Goals
February goals and daily notebook entries.
Point Whitney Field Day 26 Feb 2025
This post details activities from the field at Point Whitney for our oyster work.
E5 timeseries molecular mRNA-WGBS machine learning analysis Part 1
This post details an exploratory analysis to try out machine learning analyses to predict mRNA state from WGBS state for the E5 time series molecular project.
E5 timeseries project multiomic WGCNA Part 1
This post details my first round of analysis of correlations between gene expression (RNAseq) and methylation (WGBS) in the E5 time series molecular samples.
Testing CO2 bubbling in FTR
Today I tested the effect of CO2 bubbling in seawater on pH for Genevieve’s project.
Analysis of Goose Point growth data Part 1
This post details analysis of growth data measured by Noah K. from the Goose Point outplants from June to September 2024.
E5 deep dive lncRNA mRNA correlation networks
This post details mRNA-lncRNA correlation network analyses for the E5 deep dive expression project.
PolyIC Seed Resazurin Assay January 28 and 29 2025
This post details resazurin analyses conducted from 28-29 January 2025.
Resazurin Metabolic Assays Protocol for PolyIC Seed Testing
This post details the working protocol for PolyIC Seed tests using the resazurin metabolic assay.
January 2025 Goals
January goals and daily notebook entries.
PolyIC Seed Resazurin Assay Testing
This post details methods testing from this week for PolyIC seed resazurin testing.
Resazurin data analysis and size normalization for 10K seed project
This post details revised 10K seed resazurin metabolic rate analysis incorporating size data for metabolic rate normalization.
Oysters at FTR 8 Jan 2025
Today I moved oysters from Point Whitney to UW in FTR for lab research and testing.
Point Whitney Field Day 7 Jan 2025
This post details activities from the field at Point Whitney for our oyster work.
December 2024 Goals
December goals and daily notebook entries.
Oyster outplant fall assessment at Westcott Dec 17
Today Grace and I did an assessment of oyster survival and growth at Westcott Shellfish. This assessment is our fall time point. We will assess again in the spring.
Oyster outplant fall assessment at Goose Point Dec 11
Assessment of oyster survival and growth at Goose Point oysters. This assessment is our fall time point. We will assess again in the spring.
Oyster Tank Maintenance in FTR
This post details weekly oyster maintenance protocols for the tanks in FTR.
Larval size and symbiont cell density from Hawaii 2023 project
This post details processing of Hawaii 2023 project samples for larval size and symbiont cell density.
PolyIC spat sampling at Point Whitney 20241204
Today I went to Point Whitney to sample seed from our PolyIC project and check on our other oysters at Point Whitney.
Reorganizing oyster tanks in FTR
Today I moved all the oysters in FTR into plastic crates to organize and give the oysters more water flow.
Preliminary environmental RDA analysis for E5 physiology project
Today I ran redundancy (RDA) and variance partioning analyses to examine environmental drivers of physiology across seasons for the E5 Coral Project. he GitHub repository for this paper can be found here. Check out the README
for this project in the GitHub repository for more information.
Plans for USDA seed transfers in 2025
Today we talked with Neil Thompson at USDA to plan seed transfers for 2025.
Sanger sequencing preps for Moorea 2023 project at URI
During my visit to URI this past week I processed DNA for Sanger sequencing for species identification. These samples are from the 2023 Moorea Symbiotic Exchange project. In this project, I collected corals of three genera (Acropora, Pocillopora, Porites) including adults and recruits. We used Sanger sequencing and RFLP to identify species within these genera.
E5 metabolomics and lipidomics tissue preps
Jill and I optimized lipid and metabolite tissue preparations for the E5 project. Detailed notes are in Jill’s notebook. Jill is now starting preparations of our samples for lipid and metabolite analyses at UW.
November 2024 Goals
November goals and daily notebook entries.
Outreach event with Maritime High School Nov 12 2024
Today we hosted an outreach event with Maritime High School! We hosted ~35 students for several activities. Here is a quick overview of the activities that we did in the lab. We split the students into two groups since it was a large group.
E5 molecular timeseries metabolomics test data analysis
This post details analysis of test metabolomic samples for the E5 timeseries molecular project.
October 2024 Goals
October goals and daily notebook entries.
10K seed outplant at Baywater Shellfish
This post details outplanting 10K Seed at Baywater shellfish.
10K seed outplant preparations
This post details preparations for outplanting 10K Seed at Baywater shellfish.
Analysis of Efforts BDE oyster lab survival tests
Today I ran scripts to analyze Efforts B, E, and D survival incubations for oysters in the lab.
Larval sampling at Point Whitney 21 October
Today I sampled oyster larvae at 14 days post fertilization out at Point Whitney following broodstock PolyIC spawning.
Larval sampling at Point Whitney 15 October
Today I sampled oyster larvae at 8 days post fertilization out at Point Whitney following broodstock PolyIC spawning.
E5 molecular timeseries lipidomics test data analysis
This post details analysis of test lipidomic samples for the E5 timeseries molecular project.
Larval sampling at Point Whitney 10 October 2024
Today I sampled larvae (day 3 post fertilization) at Point Whitney.
Analysis of Effort D oyster lab survival tests
Today I ran scripts to analyze Effort D survival incubations for oysters in the lab.
Spawning at Point Whitney 7 October 2024
Today we did a broodstock immune priming treatment and spawn with oysters at Point Whitney.
Generating physiology PC1 scores for timeseries molecular work
Today I generated PC’s for each species in the E5 physiology time series to use for correlations to gene expression.
Initial analysis of resazurin metabolic rates in 10K Seed oysters
This post details initial analysis of resazurin metabolic rate measurements in 10K Seed oysters.
Plotting temperature logger data for oyster field sites
This post shows plots from temperature loggers for oyster field sites and outplant sites.
Preliminary lipidomic and metabolomics analysis of Hawaii 2023 larval data
This post details preliminary analysis of lipidomic and metabolomic data for the Hawaii 2023 larval project.
September 2024 Goals
September goals and daily notebook entries.
Point Whitney Field Day September 17 and 20 2024
Field work notebook posts from 17-20 September at Point Whitney.
Data entry for Goose Point data and schedule for incubations
This post details protocol for data entry for Goose Point oyster growth data from 9/9/2024 and schedule for oyster survival incubations next week.
Survival and growth of oysters at Goose Point in Willapa Bay
This post details activities at Goose Point from 9 September 2024 to collect survival and growth data from our June outplants.
August 2024 Goals
August goals and daily notebook entries.
10K seed resazurin survival analysis
This post details survival analysis from 10K Seed resazurin trial survivorship measurements.
Field day at Point Whitney Aug 8 2024
This post details activities at Point Whitney from 8 August 2024.
Sampling 10K seed oyster project at UW
This post details sampling for 10K seed hardening project at UW.
July 2024 Goals
July goals and daily notebook entries.
Field day at Point Whitney July 15 2024
This post details activities at Point Whitney from 15 July 2024.
Field day at Point Whitney July 10 2024
This post details activities at Point Whitney from 10 July 2024.
Field day at Point Whitney June 28 2024
This post details activities at Point Whitney from 28 June 2024.
PolyIC Immune Priming Protocols
This post describes previous protocols for PolyIC immune priming in oysters using emmersion/bath methods. We will use these protocols to design PolyIC exposure in oysters at Point Whitney.
DESeq LRT and Functional Enrichment Analysis of Mcap2020 TagSeq Data
This post details analysis of the Montipora capitata TagSeq data set using a DESeq2
likelihood ratio test approach and subsequent functional enrichment using goseq
. I previously found an error in my functional enrichment code that is corrected in this revised analysis.
Outplanting oysters at Goose Point in Willapa Bay
This post details activities at Goose Point from 25 June 2024 to outplant oysters.
Field day at Point Whitney Preparing Outplants June 24 2024
This post details activities at Point Whitney from 24 June 2024 to prepare Goose Point outplants.
June 2024 Goals
June goals and daily notebook entries.
Field day at Point Whitney June 19 2024
This post details activities at Point Whitney from 19 June 2024.
Spawning at Point Whitney June 13 2024
This post details overview of spawning activities and a general protocol for spawning at large scale at Point Whitney from 13 June 2024.
Field day at Point Whitney June 12 2024
This post details activities at Point Whitney from 12 June 2024.
Oyster survival testing for lifestage carryover project
Planning for Survivorship measurements
NCBI upload for Montipora capitata larval tolerance ITS2 sequences
This post details NCBI SRA upload of ITS2 sequences for the Montipora capitata larval thermal tolerance project on June 11 2024.
Hawaii 2023 Larval Tolerance project ITS2 Analysis Part 1
This post details download and QC for the ITS2 analysis pipeline for 2023 Hawaii Larval Thermal Tolerance project.
Upcoming oyster projects and to do lists
This post list upcoming oyster projects and next stages for our reference.
Preparing Westcott outplants at Point Whitney on June 4 2024
This post details activities at Point Whitney from 4 June 2024 and preparation of oysters for outplanting at Westcott on 7 June 2024.
Oyster outplant overview
This post shows an overview of oyster outplanting efforts for this summer.
Hatchery field day at Point Whitney May 29 2024
This post details activities at Point Whitney from 29 May 2024 trip.
May 2024 Goals
May goals and daily notebook entries.
Hatchery field day at Point Whitney May 22 2024
This post details activities at Point Whitney from 22 May 2024 trip.
Hatchery field day at Point Whitney May 16 2024
This post details activities at Point Whitney from 16 May 2024 trip.
Transfer raw sequencing data to backup Andromeda folder
This post details transfer of raw files for sequencing projects to hputnam KITT folder on Andromeda as an additional backup.
Oyster ploidy results
This post details ploidy results from Manchester (Pacific Hybreed).
DESeq2 Analysis of Montipora capitata 2023 RNAseq data
This post details DESeq2 analysis to identify differentially expressed genes for the Montipora capitata 2023 larval thermal tolerance project RNAseq. See my notebook posts and my GitHub repo for information on this project.
Hatchery field day at Point Whitney May 6 2024
This post details activities at Point Whitney from 6 May 2024 trip.
Hatchery field day at Point Whitney May 1 2024
This post details activities at Point Whitney from 1 May 2024 trip.
Alignment and assembly of RNAseq reads for Montipora capitata larval thermal tolerance 2023 project
This post details alignment and assembly steps of the bioinformatic pipeline for the Montipora capitata 2023 larval thermal tolerance project RNAseq. See my notebook posts and my GitHub repo for information on this project.
UT Sydney processing for lipidomics and metabolomics for Hawaii 2023 project
This post details lipidomics and metabolomics extraction and analysis for samples from the Montipora capitata 2023 larval thermal tolerance project at the Unviersity of Technology Sydney in Australia with Dr. Jennifer Matthews.
April 2024 Goals
April goals and daily notebook entries.
QC of top off RNAseq files for Montipora capitata larval thermal tolerance 2023 project
This post details QC of the Montipora capitata 2023 larval thermal tolerance project RNAseq files from second delivery of top off sequencing. See my notebook posts and my GitHub repo for information on this project.
Raw sequence downloads and NCBI SRA uploads for M. capitata larval thermal tolerance project top off sequencing second upload
This post details the NCBI Sequence Read Archive upload for my Montipora capitata 2023 larval thermal tolerance project. See my notebook posts and my GitHub repo for information on this project.
Hatchery field day at Point Whitney April 3 2024
This post details activities at Point Whitney from 3 April 2024 trip.
KAPA bead clean-up protocol for removal of primer dimers from PCR product
This post details a protocol for KAPA bead clean up of PCR product to remove primer dimers.
Pocillopora and Porites Species ID Sanger Sequencing and RFLP protocol
This post details protocols for Sanger Sequencing and RFLP assays for species identification of Porites and Pocillopora from gDNA.
ITS2 amplicon PCR and preparation for sequencing 20240326
The post details ITS2 amplicon PCR amplificaiton and preparation for sequencing.
Protocols used during URI 2024 visit
List of protocols used in the lab at URI for lab-a-thon in March 2024!
March 2024 Goals
March goals and daily notebook entries.
Sequence depth subsampling test with Mcap2020 ITS2 dataset
This post details test for subsampling thresholds in the Montipora capitata early life history timeseries dataset. The purpose of these tests is to determine the minimum read depth to detect differences between treatment groups for future sequencing runs.
Prepare data
Load metadata.
#create metadata and load
Metadata<-read.csv("Mcap2020/Data/ITS2/ITS2_Metadata.csv")
rownames(Metadata) <- Metadata$sample_name
Metadata <- Metadata %>%
select(code, hpf, group, lifestage)
Metadata <- as.matrix(Metadata)
Metadata <- sample_data(data.frame(Metadata))
Load profile level data.
#load data for taxonomy
tax0 <- read_tsv(
file = "Mcap2020/Data/ITS2/mcap.profiles.absolute.abund_and_meta.txt",
n_max = 6) %>%
dplyr::select(-2) %>%
gather(UID, value, -1) %>%
spread(1, value) %>%
clean_names()
tax1 <- as.matrix(tax0[, -1], dimnames = list(tax0$uid, colnames(tax0[-1])))
rownames(tax1) <- tax0$uid
tax <- tax_table(tax1)
#load data for count matrix
otu0 <- read_tsv(
file = "Mcap2020/Data/ITS2/mcap.profiles.absolute.abund_and_meta.txt", col_names = TRUE)
list<-c("UID", "sample_name", "8", "9")
colnames(otu0)<-list
otu0<-otu0%>%
select(-1) %>%
dplyr::slice(7:n()) %>%
mutate_at(2:ncol(.), as.numeric)
otu1 <- as.matrix(otu0[, -1])
rownames(otu1) <- otu0$sample_name
otu <- otu_table(otu1, taxa_are_rows = FALSE)
#combine to phyloseq object
coral <- phyloseq(otu, tax, Metadata)
coral
Note that taxa 8 is Clade C and taxa 9 is Clade D.
Next load the data for coral strain level information.
#gather the taxonomy names
taxnames <- read_tsv(
file = "Mcap2020/Data/ITS2/mcap.seqs.absolute.abund_only.txt",
n_max = 0) %>%
select(-1) %>%
names(.)
#extract clade letter
tax0 <- data_frame(
DIV = taxnames,
clade = str_extract(DIV, "[A-Z]")
)
tax1 <- as.matrix(tax0)
rownames(tax1) <- tax0$DIV
tax <- tax_table(tax1)
otu0 <- read_tsv(
file = "Mcap2020/Data/ITS2/mcap.seqs.absolute.abund_and_meta.txt") %>%
select(-1, )
otu1 <- as.matrix(otu0[, 37:113])
rownames(otu1) <- otu0$sample_name
otu <- otu_table(otu1, taxa_are_rows = FALSE)
coralDIV <- phyloseq(otu, tax, Metadata)
coralDIV
Now save the object.
save(coral, coralDIV, file = "Mcap2020/Data/ITS2/ITS2_phyloseq.RData")
Build DIV Data
Load the data.
load("Mcap2020/Data/ITS2/ITS2_phyloseq.RData")
coralDIV
View the number of sequence counts in our dataset.
Samps<-read_tsv(file = "Mcap2020/Data/ITS2/mcap.seqs.absolute.abund_and_meta.txt")
hist(Samps$post_taxa_id_absolute_symbiodiniaceae_seqs, breaks=30)
Samps$post_taxa_id_absolute_symbiodiniaceae_seqs
We have >10,551 sequences for all of our samples.
Generate tree.
random_tree = rtree(ntaxa(coralDIV), rooted=TRUE, tip.label=taxa_names(coralDIV))
Merge phyloseq data.
phylo_coral_DIV = merge_phyloseq(coralDIV, Metadata, random_tree)
phylo_coral_DIV
Filter out samples with low numbers in groups (n=1 per group) from phyloseq object.
phylo_coral_DIV<-ps_filter(phylo_coral_DIV, lifestage != "Metamorphosed Polyp (183 hpf)")
phylo_coral_DIV<-ps_arrange(phylo_coral_DIV, lifestage)
Reorder lifestage.
levels(as.factor(sample_data(phylo_coral_DIV)$lifestage))
sample_data(phylo_coral_DIV)$lifestage = factor(sample_data(phylo_coral_DIV)$lifestage, levels = c("Egg (1 hpf)","Embryo (5 hpf)","Embryo (38 hpf)","Embryo (65 hpf)", "Larvae (93 hpf)", "Larvae (163 hpf)", "Larvae (231 hpf)", "Metamorphosed Polyp (231 hpf)", "Attached Recruit (183 hpf)", "Attached Recruit (231 hpf)"))
levels(as.factor(sample_data(phylo_coral_DIV)$lifestage))
Assign object to a shorter name.
GP1 = phylo_coral_DIV
GP1
Display sample sequencing depth.
min(sample_sums(GP1))
We will attempt subsampling at the minimum count (10,551 sequences) and in steps decreasing from 10551, 8000, 6000, 4000, 2000, 1000, 500.
DIV level analysis
E5 POC and POR Species ID PCR and RFLPs
This post details protocls and results from identifying species of Porites and Pocillopora samples for the E5 RoL project.
Correcting subsampling error in Mcap2020 ITS2 code and revise results
This post describes correcting code and revising analyses for Montipora capitata 2020 developmental time series project.
Hatchery day at Point Whitney to continue seed stress exposures
This post details seed exposures at Point Whitney on 3/19.
Process to apply for US CITES export permit
This post details the process I used to apply for a CITES export permit with the US Fish and Wildlife management authority.
Washington Sea Grant Shellfish Growers Meeting Notes
This post contains my notes and thoughts from attending the Washington Sea Grant Conference for Shellfish Growers on March 11-12 2024.
Analysis of Variance Simultaneous Component Analyses ASCA for CEABIGR project
This post details Analysis of Variance Simultaneous Component Analyses (ASCA) for the CEABIGR project.
Point Whitney field day to start individual growth experiment and plan for new seed exposure work
This post details field day and project design on 5 March 2024 at Point Whitney.
Lifestage Carryover Project Sampling
This post details sampling on 28 February 2024 at Point Whitney.
WGCNA Attempt 2 for ceabigr project exon expression data
Today I played around with another attempt at WGCNA analyses to look at exon expression data for the ceabigr project.
Prepping equipment and oysters for Lifestage Carryover project sampling day
This post details preparations for oyster sampling for Lifestage Carryover project.
February 2024 Goals
February goals and daily notebook entries.
QC of RNAseq files for Montipora capitata larval thermal tolerance 2023 project
This post details initial QC of the Montipora capitata 2023 larval thermal tolerance project RNAseq files. See my notebook posts and my GitHub repo for information on this project. Also see my notebook post on sequence download and SRA upload for these files.
Raw sequence downloads and NCBI SRA uploads for M. capitata larval thermal tolerance project
This post details the NCBI Sequence Read Archive upload for my Montipora capitata 2023 larval thermal tolerance project. See my notebook posts and my GitHub repo for information on this project.
Oyster lifestage carryover project growth preliminary analysis
Post detailing preliminary analysis of oyster growth data in the USDA/WSG lifestage carry over project.
Hatchery Day at Point Whitney to Check Lifestage Carryover Project
Hatchery day at Point Whitney for the USDA & WSG Lifestage Carryover Project.
WGCNA Attempt 1 for ceabigr project exon expression data
Today I played around with WGCNA analyses to look at exon expression data for the ceabigr project.
Oyster USDA WSG Project Planning 5 Feb 2024
Post detailing meeting notes and design considerations for USDA and WSG projects from 2/5/2024.
Revising E5 timeseries results - restructuring figures, filtering, and haplotypes
THis post details updates to the E5 time series analysis. The GitHub repository for this paper can be found here. Check out the README
for this project in the GitHub repository.
Planning WSG USDA sample sizes and equipment for spring oyster rearing
This post details experimental design thoughts and brainstorming for the WSG and USDA project efforts.
WSG USDA Hatchery Day - Assessing lifestage carry over project
Hatchery day at Point Whitney for the USDA & WSG projects.
January 2024 Goals
January goals and daily notebook entries.
Moorea 2023 Symbiotic Nutritional Exchange Project Daily Entries
This post details daily entries for the Fall 2023 Moorea Field Expedition.
December 2023 Goals
December goals and daily notebook entries.
October 2023 Goals
October goals and daily notebook entries.
Ceabigr correlation matrices attempt
Genes-SNPs-methylation correlation first attempt for CEABIGR project
================
September 2023 Goals
September goals and daily notebook entries.
Larval rearing at Point Whitney
Today, we moved larvae that were spawned and reared at Pt. Whitney hatchery (~48 hrs old) into HUDL systemsfor the Roberts Lab USDA oyster project.
August 2023 Goals
August goals and daily notebook entries.
Trial oyster strip spawning at Point Whitney
Today, Steven and I went to Point Whitney to trial strip spawning and fertilization for the Roberts Lab USDA oyster project.
F1F2 project data analysis Hawaii 2023
This post details respirometry data analysis of the Montipora capitata F1F2 project at the Hawaii Institute of Marine Biology (HIMB) in June 2023.
July 2023 Goals
July goals and daily notebook entries.
Hawaii 2023 Coral Spawning and Field Expedition Daily Entry
This post includes the full notebook for June-July 2023 Montipora capitata coral spawning and field expedition in Hawaii at the Hawaii Institute of Marine Biology. These notebook posts by A. Huffmyer are updated in order of most recent to oldest.
SDR Microplate Respirometry Protocol
This protocol details the step-by-step use of PreSens/Loligo Microplate respiration system for coral larvae.
Sanger Sequencing Training
Introduction to Sanger sequencing and training for coral species identification.
June 2023 Goals
June goals and daily notebook entries.
E5 Deep Dive RNAseq WGCNA Analysis
This post details WGCNA preliminary analysis for the E5 Deep Dive Project.
May 2023 Goals
May goals and daily notebook entries.
Mcap 2021 Stable Isotope Metabolomics Analysis
This post details the initial stable isotope metabolomics analysis for the Montipora capitata 2021 larval temperature exposure.
April 2023 Goals
April goals and daily notebook entries.
Revising E5 Time Series Multivariate Plasticity Analysis
This post details revisions to calculations for multivariate physiological plasticity analysis for the E5 Rules of Life project.
E5 Deep Dive RNAseq Count Matrix Analysis
This post details analysis and bioinformatic steps to generate a gene count matrix from RNAseq data for the E5 Deep Dive Project.
Mcapitata Larval Temperature Experiment Data Analysis
This post details analysis of survival, settlement, physiology, and environmental data for the 2021 Montipora capitata larval temperature project.
March 2023 Goals
March goals and daily notebook entries.
2023 UW Software Carpentry Workshop in Terminal Git and R
Workshop: Software Carpentry in R - Terminal, GitHub, and R
February 2023 Goals
February goals and daily notebook entries.
Intro to DVC Workshop
Today, I attended a workshop through the UW eScience Data Science postdoc group for an introduction to DVC, a version-control platform.
TidyTuesday Exercises
This post is a running log of miscellaneous coding and TidyTuesday exercises!
January 2023 Goals
January goals and daily notebook entries.
Integrative analysis for Montipora capitata developmental time series
This post details integrative analysis and plotting for response variables in the Montipora capitata 2020 developmental time series.
Analyzing TagSeq data with new annotation
This post details re-analyzing TagSeq data for the 2020 M. capitata developmental timeseries project to a more recent v3 genome with annotation.
Revising Figures for Mcapitata Development 2020 Project
This post shows newly revised figures and revisions to analysis for the 2020 Montipora capitata development project.
Mcapitata Development 16S Analysis - Mothur pipeline visualizations
This post details recent updates to the Montipora capitata developmental time series 16S analysis.
December 2022 Goals
Writing
- Revise Montipora capitata 2020 time series figures
- Conceptual
MetabolomicGene ExpressionPhysiologyIntegration
- Revise Montipora capitata 2020 time series text to PNAS short format
- Work with Emma to revise results of E5 time series manuscript
Reanalyze TagSeq data to new M. capitata genome
Analyzing Acropora larval metabolism experiment respirometry data
This post details analysis of respirometry data for the Acropora pulchra larval metabolism experiment in Moorea in Oct 2022.
Symbiont gene expression in Mcap2020 developmental time series
This post details alignment of TagSeq sequences from the Mcap2020 developmental time series project to the symbiont genome. We will evaluate the results of this alignment to see if we have enough sequences to analyze symbiont-specific gene expression.
Analyzing Environmental Data - Acropora larval metabolism 2022
This post details environmental measurements analysis for the 2022 Acropora larval metabolism experiment from the Moorea 2022 Field Expedition.
SRA Uploads 10 November 2022
This post details the NCBI Sequence Read Archive upload for Ariana Huffmyer’s Montipora capitata 2020 early life history timeseries project.
Moorea 2022 Coral Spawning and Field Expedition Daily Entry
This post includes the full notebook for Sept-Oct 2022 Acropora coral spawning and field expedition in Moorea, French Polynesia. These notebook posts by A. Huffmyer are updated in order of most recent to oldest.
November 2022 Goals
Writing
- Full draft of E5 results section for the 2020 time series project
Submit proofs for Pocillopora acuta diversity paper~- Revise Montipora capitata 2020 time series metabolomics and gene expression figures and associated text
October 2022 Goals
Writing
- First draft of E5 time series results section and outline of discussion section
Submit proofs for science education paper- Start Montipora capitata 2020 time series revisions
September 2022 Goals
Writing
- First draft of E5 time series results section and outline of discussion section
Submit revision for Pocillopora acuta genetic diversity paperGo over Montipora capitata 2020 time series revisions with HP- Start Montipora capitata 2020 time series revisions
E5 Multivariate Physiological Plasticity Analysis
This post details multivariate physiological plasticity analysis for the E5 Rules of Life project.
August 2022 Goals
Writing
Finish and send final draft of Montipora capitata ontogeny 2020 manuscript to co-authors- First draft of E5 time series manuscript by end of August with full results and outline of discussion section
Submit final revision for science education manuscriptWrite methods and results section of Montipora capitata larval temperature exposure 2021 project- Submit revision for Pocillopora acuta genetic diversity paper
Montipora capitata spawning and larval rearing protocol
This protocol details the methods for collecting Montipora capitata bundles during spawning, fertilizing gametes, and rearing and settling larvae in Hawai’i during the summer months.
Stable Isotope Metabolomics Larval Protocol
This protocol details the step-by-step process for incubations for stable isotope metabolomics for coral larvae.
June 2022 Goals
Writing
- Write results of Montipora capitata development manuscript
- Draft results of E5 time series manuscript
May 2022 Goals
Writing
Methods and results of Montipora capitata development manuscript- Submit final revision of science identity manuscript (delayed until August 2022)
Multi-Omic Integration Analysis Part 1
This post details preliminary analyses of multi-omic datasets collected in the Montipora capitata early life history time series project.
Larval Size Photographs Protocol
This protocol describes the process for taking photographs of preserved coral larvae for measurement of larval size (volume, surface area, length, etc.).
Symbiont Cell Counts Protocol
This protocol details symbiont cell counts in coral larval tissue samples. This protocol is modified from the E5 cell counts protocol.
Stable Isotope Metabolomics Extraction Protocol
This protocol details metabolite extraction from coral larval samples labeled with stable isotopes (C13 bicarbonate) and control samples (C12 bicarbonate).
Protein Protocol
This protocol details quantification of soluble protein from coral larval samples. This protocol is modified from the E5 Protein Protocol.
Montipora capitata 2021 larval temperature experiment sample processing
This post details sample processing completed in April 2022 for the 2021 M. capitata larval thermal exposure experiment conducted in Hawaii.
Chlorophyll Content Protocol
This protocol details chlorophyll measurement in coral larval tissue samples. This protocol is modified from the E5 chlorophyll protocol.
Carbohydrates Protocol
This protocol details quantification of carbohydrate content in coral larvae in 96-well plates modified from the Bove Baumann protocol and the Putnam Lab carbohydrate protocol.
Putnam Lab Oyster 16S Analysis in Mothur
This post details 16S analysis of the Putnam Lab oyster project using the Mothur pipeline based on A. Huffmyer’s pipeline here.
March 2022 Goals
Writing
- Write results of Montipora capitata development manuscript
- Start discussion of Montipora capitata development manuscript
Comparing TagSeq between genome assembly V1 and V2
This post details analysis of TagSeq data from previous alignment to M. capitata version 1 assembly and version 2 assembly.
February 2022 Goals
Writing
Finish methods of Montipora capitata development manuscript- Write results of Montipora capitata development manuscript
- Start discussion of Montipora capitata development manuscript
Comparing QIIME2 and Mothur 16S QC and Filtering
This post details QC and filtering steps that were done in both Mothur and QIIME2 to compare the sequence QC results.
Analyzing 16S Mothur Results in R
This post details analyzing relative abundance and diversity metrics in R output from mothur analysis of 16S data for the 2020 early life history Montipora capitata time series.
Metabolomics WGCNA Analysis Part 2
This post details continued analysis of metabolomics data for the 2020 M. capitata developmental time series with WGCNA.
16S Pipeline in Mothur
This post details 16S data analysis using the Mothur pipeline for the 2020 Montipora capitata developmental time series.
January 2022 Goals
Publications
Revise and submit intraspecific diversity paperWrite methods for Pocillopora acuta thermal exposure paperOutline revisions for Life History energetics perspective paperOutline results section of E5 timeseries manuscript- Finish methods and write results of Montipora capitata development manuscript
Mcapitata Development 16S Analysis in QIIME2 (Part 3)
This post details QC and QIIME analysis for the 16S analysis adapted from the pipeline developed by Emma Strand.
Mcapitata Development ITS2 Analysis Part 2
This post details SymPortal analysis for the ITS2 analysis pipeline modified from Kevin Wong pipeline.
Mcapitata Development ITS2 Analysis Part 1
This post details MultiQC for the ITS2 analysis pipeline. 16S files are analyzed in a separate post.
Mcapitata Development 16S Analysis Part 2
This post details QC and QIIME analysis for the 16S analysis adapted from the pipeline developed by Emma Strand.
Mcapitata Development 16S Analysis Part 1
This post details MultiQC for the 16S analysis pipeline adapted from the pipeline developed by Emma Strand. In this post there is information for moving/managing ITS2 sequences, but this post details preliminary analysis of 16S. ITS2 files will be analyzed in a separate post.
Pocillopora acuta Symbiont Integration Moorea December 2021
This post details all activities in Moorea in December 2021 for Symbiont Integration project for the study species Pocillopora acuta.
ITS2 and 16s Extractions
This posts describes extraction protocols for ITS2 and 16s sequencing for the 2020 Montipora capitata developmental time series.
December 2021 Goals
Publications
- Revise and submit intraspecific diversity paper
Finish revisions and submit larval thermal conditioning paper- Outline revisions for Life History energetics perspective paper
E5 Environmental Timeseries Analysis Part 3
Environmental data analysis for the E5 Rules of Life Project continued.
E5 Time Series Data QC
This posts describes the QC process from November 2021 for the E5 Rules of Life timeseries data.
E5 Environmental Timeseries Analysis Part 2
This post continues analysis of environmental time series data for the E5 Rules of Life Project.
E5 Environmental Timeseries Analysis Part 1
This post details environmental time series QC and plotting for the E5 Rules of Life project.
Metabolomics WGCNA Analysis Part 1
This posts describes weighted gene co-expression analysis (WGCNA) applied to metabolmoics data from the 2020 Montipora capitata early life history developmental time series.
November 2021 Goals
Proposals and applications
Submit education paper revisions to CBE - Life Sciences Education (November 9)Submit Science Incubator proposal (November 10)Submit NSF OCE proposal (November 12)Prepare E5 time series talk for Moorea LTER Annual Meeting in early December
Pocillopora Larval Collection June 2021
Post describing Pocillopora larval collection for collaborative projects with Carneige and Rutgers in June 2021.
Larval Settlement Mcapitata June 2021
Post detailing larval settlement and maintenance in June 2021 for M. capitata spawning.
Isotope Time Series Data Collection June 2021
Post detailing stable isotope time series data collection for methods optimization and development for coral larvae in collaboration with Rutgers University.
Mcapitata Temperature Exposure and Design June 2021
Post detailing temperature exposure and experimental design for M. capitata larval temperature experiment in June 2021.
Mcapitata Survival and Experiment Maintenance June 2021
Post detailing survival measurements and experimental maintenance in larval temperature experiment with M. capitata in June 2021.
Mcapitata Spawning and Fertilization June 2021
Collection, fertilization, and rearing of Montipora capitata spawned gametes during the June 2021 spawning at the Hawaii Institute of Marine Biology.
Mcapitata Sampling and Data Collection June 2021
Post details sampling and data collection for M. capitata larval temperature exposure experiment in June 2021.
Mcapitata Equipment Setup 2021
Post detailing tank and experimental set up for Montipora capitata coral spawning in Hawaii in June 2021.
Mcapitata Culture Maintenance June 2021
Post detailing culture maintenance of embryos of Montipora capitata during June 2021 larval temperature experiment and spawning.
Mcapitata Baseline Sampling June 2021
Post detailing sampling of Mcapitata larvae collected as baseline samples prior to temperature experiment in June 2021.
Mcapitata 2020 Early Life History Sample Processing
This entry details sample processing for Mcapitata 2020 early life history samples for metabolomics, larval size and symbiont cell densitites, and RNA excxtraction for TagSeq.
Ahyacinthus Early Life History Respirometry
This entry describes the sampling and respirometry data collection for Acropora hyacinthus in Moorea, French Polynesia at CRIOBE and Gump Research Stations.
Mcapitata Respiration and Photosynthesis Early Life History July 2020
This entry lists the runs and data collection for early life history respirometry (photosynthesis and respiration) in early life stages (larvae, recruits, and juveniles) of Montipora capitata in July 2020.
Mcapitata Larval Rearing and Settlement July 2020
This notebook entry details methods for larval rearing and settlement for Montipora capitata early life history in July 2020. Sampling of these life stages is described in additional notebook entries.
Mcapitata July 2020 Embryo Larvae Recruit Sampling
This entry details the sampling and collection of embryos, larvae, and recruits of Montipora capitata during July-Aug 2020 spawning period.
Mcapitata Early Life History Respirometry Protocol
This entry describes the protocol for measuring photosynthesis and respiration in early life history stages of Montipora capitata.
Mcapitata July 2020 Sampling Protocol
This protocol provides an overview of sampling early life history stages for Montipora capitata in July-August 2020.
Mcapitata Spawning and Fertilization July 2020
Collection, fertilization, and rearing of Montipora capitata spawned gametes during the July 2020 spawning at the Hawaii Institute of Marine Biology in collaboration with C. Drury and J. Hancock in the Gates Coral Lab.