Posts

Author

Sarah Tanja

Modified

September 1, 2025

Master’s Thesis Committee Meeting #3

Progress check-in on analyses
committee
presentations
May 6, 2025
Sarah Tanja

Submitted NGS 16SrRNA sequences to NCBI SRA

Backing up raw sequences from mim_c
lab records
code
Watch this 10min video tutorial: How to Submit to SRA, A Beginner’s Guide
December 13, 2024
Sarah Tanja

Backup your work

using rsync
workflow
It’s good practice to have an active work server that you push code to GitHub, and a backup server that you’re not working in for the large files you generate. In case you…
November 4, 2024
Sarah Tanja
 

Make a secret tunnel

use .ssh/config file to connect to a remote server
code
Open a terminal ( I opened my WSL Ubuntu terminal 🐧) and make a .ssh directory in the home directory, and then open the nano text editor to write a config file in the .ssh…
November 4, 2024
Sarah Tanja

Submitting NGS sequences to NCBI SRA

Backing up raw sequences from Azenta
learning journey
code
So you got an email from Azenta saying your files are ready for download! Exciting! It’s the moment we’ve been waiting for. What next??
October 8, 2024
Sarah Tanja

Transfer data files from Azenta to a local server

Getting raw NGS fastq sequence files off Azenta Genewiz server to a local server using Command Line and SFTP
learning journey
code
Azenta will email you to notify you that your project is complete and is being uploaded to your account on the Azenta sFTP server, where it will be available for download…
October 8, 2024
Sarah Tanja
 

Bioinformatics Pipeline Roadmap

Transcriptomics analysis of RNA-seq data from embryonic development of Montipora capitata rice corals exposed to PVC leachate
code
coral
We’ve extracted totalRNA and shipped it to Azenta for sequencing… so what happens next? How did we go from working with microcentrifuge tubes in the lab to large files on…
October 7, 2024
Sarah Tanja
 

Summary of previous research on microplastic leachate exposure in marine invertebrate embryonic development

In sea urchin and mussel model organisms
learning journey
coral
(jimenez-guri2023?) either exposed adult sea urchins Paracentrotus lividus to excessively high1 levels of PVC leachate or filtered seawater control for 2 weeks, and then…
October 7, 2024
Sarah Tanja

Figure 12. Taken from Okubo et al. 2013

Ontogenetic Development of Montipora capitata

learning journey
coral
Montipora capitata corals are taxonomically classified in the Domain Eukaryota, Kingdom Animalia, Phylum Cnidaria, Class Hexacorallia, Order Scleractinia, Family…
September 30, 2024
Sarah Tanja
 

Grants & Fellowships

A running list of grants and fellowships to keep an eye on
stats
coral
Smithsonian fellowships are offered to individuals who design and develop proposals to conduct independent research.
September 9, 2024
Sarah Tanja

Nikon scope pictures annotation & data collection

Annotating images of embryonic development of Montipora capitata rice corals exposed to PVC leachate
protocols
coral
This guide is meant to be a checklist for annotating categories of embryonic development in Montipora capitata using NIS-Elements BR.
September 9, 2024
Sarah Tanja
 

Timeline & Goals Planning

committee
goals
This is a timeline of goals and progress made toward wrapping up my Master’s Thesis at UW SAFS.
September 8, 2024
Sarah Tanja
 

Statistics for embryo scope data

Exploring data from embryonic development of Montipora capitata rice corals exposed to PVC leachate
stats
coral
What information can we get from looking at the Montipora capitata embryos that were exposed to varying levels of PVC leachate (High: 1mg/L, Mid: 0.1mg/L, Low: 0.01mg/L)?…
September 6, 2024
Sarah Tanja
 

Nikon scope pictures & slide preservation protocol

For capturing embryonic development of Montipora capitata rice corals exposed to PVC leachate
protocols
Watch ’Mounting Your Specimen’ by Dr. Terry Bruce of Clemson University on YouTube
September 3, 2024
Sarah Tanja
 

26-Aug-2024 Embryo RNA Extractions

lab records
8C9F, 9C9F = 89C91
August 26, 2024
Sarah Tanja
 

23-Aug-2024 Embryo RNA Extractions

lab records
4L14F, 5CL14F, 6L14HF = 456L14
August 23, 2024
Sarah Tanja
 

21-Aug-2024 Embryo RNA Extractions

lab records
1C14F, 2C14F, 3C14HF = 123C14
August 21, 2024
Sarah Tanja
 

20-Aug-2024 Embryo RNA Extractions

lab records
1H9F, 2H9F, 3H9F = 123H9
August 20, 2024
Sarah Tanja
 

19-Aug-2024 Embryo RNA Extractions

lab records
4H9F, 5H9F, 6H9F = 456H9
August 19, 2024
Sarah Tanja
 

16-Aug-2024 Embryo RNA Extractions

lab records
1L4F, 2L4F, 3L4F = 123L4
August 16, 2024
Sarah Tanja

15-Aug-2024 Embryo RNA Extractions

lab records
4C14F, 5C14F = 45C14
August 15, 2024
Sarah Tanja

14-Aug-2024 Embryo RNA Extractions

lab records
1C4F, 2C4F, 3C4F = 123C4
August 14, 2024
Sarah Tanja

13-Aug-2024 Embryo RNA Extractions

lab records
coral
1C9F, 2C9F, 3C9F = 123C9F
August 13, 2024
Sarah Tanja

12-Aug-2024 Embryo RNA Extractions

lab records
6C14F (single sample ~10 embryos)
August 12, 2024
Sarah Tanja

M. Capitata Embryo DNA/RNA Extractions Protocol

protocols
coral
For inspiration checkout:
August 9, 2024
Sarah Tanja
 

HOBO logger calibrations

Two loggers per temperature bath (2 ambient, 2 hot)
protocols
records
On July 10th I calibrated the HOBO logs to a Kessler NIST K750 RTD Thermometer and an apogee instruments underwater quantum flux PAR meter.
July 10, 2024

Bench Incubation

Lab bench records and environmental logs for the development of Montipora capitata embryos exposed to PVC leachate
protocols
records
On July 5th, 6th, and 7th 2024 we conducted an ecotox assay on the development of Montipora capitata coral embryo development under exposure to PVC leachate at nominal…
July 9, 2024

Coral collections & tank acclimation protocol

For spawning of Montipora capitata rice corals
protocols
records
Describe the Montipora capitata coral colony collections under State of Hawai`i SAP2024-35 and tank acclimation prior to spawn night research activities in June & July of…
July 9, 2024
Sarah Tanja
 

Spawn night protocol

For embryonic development of Montipora capitata rice corals
protocols
This spawn night checklist was used on July 5th, 6th and 7th 2024 at the Hawaiian Institute of Marine Biology (HIMB) on Moku o Loe in Kaneohe Bay, Oahu. The overarching goal…
July 9, 2024
Sarah Tanja
 

Experiment Log

coral
Kat and Callum collected 10 distinct Montipora capitata colonies of approximately 30cm in diameter from Kaneohe Bay, Hawaii under permit
July 9, 2024
Sarah Tanja

Extracting & measuring chlorophyll a & c2 concentrations

… from an anemone-hosted symbiotic dinoflagellate using a ThermoFischer Nanodrop 2000c
protocols
anemones
This protocol draws heavily (and almost exclusively!) from the awesome method paper, “Its What’s on the Inside That Counts: An Effective, Efficient, and Streamlined Method…
May 23, 2024
Sarah Tanja

Single stressor leachate exposure summary

A 48 hour exposure to polyvinyl chloride (PVC) leachate and to aged polypropylene (PP) leachate
lab records
This summary serves as a broad overview and notes of the acute (48hour) single stressor polyvinyl chloride (PVC) and polypropylene (PP) leachate exposure to Anthopleura…
May 3, 2024
Sarah Tanja

All about the aggregating anemone

What, where, who studies it, how, and why!
learning journey
anemones
Anthopleura elegantissima are clonal intertidal anemones that can form flexible symbiotic partnerships with different single-celled algae which provide supplemental sugars…
May 2, 2024
Sarah Tanja
 

Anemone Leachate Heat Experiment Recipe

anemones
protocols
Collect anemones
April 23, 2024
Sarah Tanja

How to make a custom respirometry chamber

protocols
anemones
I had to make some custom respirometry chambers for my experiment. Here’s the requirements I needed to meet, and how I did it!
April 22, 2024
Sarah Tanja

Puget Sound Microplastics

learning journey
What are the commonly measured concentrations of microplastics in Puget Sound, Washington? This goal of this objective is to understand the environmentally relevant range of…
April 15, 2024
Sarah Tanja
 

Field collection at Constellation Park, Alki, West Seattle

anemones
lab records
On Saturday, March 30th, 2024 Kip and I collected Anthopleura elegantissima from Constellation Park near Alki in West Seattle, Washington under WDFW scientific collection…
March 30, 2024
Sarah Tanja

Leachate preparation & dilution protocol

Modified from the lab protocol of Dr. Francesco Saliu and Valerio Isa
protocols
In order to study the effects of microplastic leachate we have to be able to re-create it in a controlled and defined way. For this, I partnered with Dr. Francesco Saliu and…
March 26, 2024
Sarah Tanja

Field collection at Owens Beach, Point Defiance Park, Tacoma

anemones
lab records
On Monday, March 18th, 2024 we collected Anthopleura elegantissima from Owen’s Beach at Point Defiance Park in Tacoma, Washington under WDFW scientific collection permit Tanj…
March 18, 2024
Sarah Tanja

Daily Lab Log

Enter at your peril; This one is for me, not you
daily log
Received confirmation that RNA is in line for QAQC
February 22, 2024
Sarah Tanja

Experimental tank setup

protocols
anemones
Hydra 32HD manual
February 9, 2024
Sarah Tanja

Measuring photosynthesis

Understanding & Operating the Walz Diving-PAM-II
learning journey
anemones
Photosynthesis is magic. Four proteins embedded in a delicate lipid membrane turn light into sugar. It’s energy transformation! The process by which light energy is…
February 5, 2024
Sarah Tanja

Tides & WX Station Data

How to use the rnoaa package
learning journey
“Air temperature and tide data Air temperature and tide level data was obtained from various sources depending on the location. Hourly temperature and tide data for Toke…
February 5, 2024
Sarah Tanja

Anemone Project Planning

anemones
The objective of this study is to examine the combined effects of thermal stress and marine microplastic leachate on photosynthetic efficiency, microbiome community, and…
January 2, 2024
Sarah Tanja

Pseudoreplication & Control

How to design a manipulation experiment
learning journey
“the use of inferential statistics to test for treatment effects with data from experiments where either treatments are not replicated (though samples may be) or replicates…
December 6, 2023
Sarah Tanja

How I created & maintain my open lab notebook using Quarto, Git & RStudio

code
learning journey
follow happy git for the useR
December 6, 2023
Sarah Tanja

Phthalates around the World

learning journey
What are the common concentrations (ug/L) of phthalates measured in seawater around the world? This goal of this objective is to understand the environmentally relevant…
November 29, 2023
Sarah Tanja

Master’s Thesis Committee Meeting #2

Options for addressing the need for a solvent control
committee
Introduce issue with lack of solvent control in experimental design - 5 mins
November 19, 2023
Sarah Tanja
 

Master’s Thesis Progress

learning journey
committee
SAFS Masters Thesis Milestones are laid out here
November 19, 2023
Sarah Tanja
 

Making PAE treatments and controls

protocols
I used the EPA 506 phthalate esters mix 1, which comes as a 1mL ampule vial with a glass break-off cap. It includes 6 common phthalates each at a concentration of \(500\mu…
November 14, 2023
Sarah Tanja
 

Workflow with Git

For all the times I accidentally commit a file that is too big
workflow
.gitignore cannot filter files by size — it only filters by path patterns, like filenames, extensions, or directory names. It doesn’t support dynamic criteria like file…
November 5, 2023

Dual DNA & RNA Extraction Protocol

protocols
The aim of this protocol is to take coral fragments that have been snap-frozen in liquid nitrogen and extract both DNA for downstream archaea & bacteria microbiome 16S…
August 23, 2023
Sarah Tanja

Nanodrop plot results

The RNA Inhibitors

A tragic saga of continued troubles
lab records
After shipping 20 samples to the University of Texas at Austin GSAF for TagSeq on June 7th 2023, I got a message back from them on June 28th 2023:
August 22, 2023
Sarah Tanja
 

Getting Started with QIIME2 and Jupyter Lab

Working from a Windows OS and connecting via VPN to a remote server
code
learning journey
Sometimes it seems the hardest part about developing a new workflow is deciding where to put it! As I start working on analyzing my microbiome data, I need to have a Linux…
August 10, 2023
Sarah Tanja
 

Target Journals for Submitting Manuscripts

learning journey
Impact Factor 8.9
July 27, 2023
Sarah Tanja
 

Phthalate exposure to coral embryos methods

M. capitata embryo development and EPA 506 pthalate mix 1 acute exposure experimental methods
lab records
protocols
Plasticizers are a suite of chemicals added to plastic consumer products to increase flexibily. The most widely used plasticizers are phthalate acid esters (PAEs). PAE’s are…
June 22, 2023
Sarah Tanja
 

Choosing 16S Primers for M. capitata microbiome

learning journey
” Indeed Cruaud et al. (2014) and Fouhy et al. (2016) show that primer choice has a far deeper influence on microbial community than extraction method, although they did…
June 8, 2023
Sarah Tanja

DNA/RNA Extractions Overview

lab records
Qubit RNA BR Assay Kit The Qubit RNA BR (Broad-Range) Assay Kit, when used with the Qubit Fluorometer, provides an accurate and selective method for the quantitation of RNA…
May 23, 2023
Sarah Tanja

Environmental Landscape of an Intertidal Heat Wave

Using NOAA National Data Buoy Center (NDBC) to map air and water temperatures in Commencement Bay, Tacoma, WA, during the June 2021 Puget Sound heat wave
I searched the NDBC map for the stations closest to my collection site at Owens Beach, Point Defiance Park in Commencement Bay, Tacoma.
Invalid Date
Sarah Tanja

Dual DNA & RNA Extractions for Montipora capitata coral

lab records
These lab extractions follow the Dual DNA & RNA Extraction Protocol with any deviations, exceptions, or notes explained in detail.
April 25, 2023
Sarah Tanja

Figure 2. ‘Weathering processes of poorly reversible plastic pollution in the environment.Weathering proceeds along two co-occurring and synergistic pathways offragmentation and release of chemicals, and biofouling and oxidation.’ from Macleod et al. 2021

Master’s Thesis Committee Meeting #1

committee
Introduction - 5 mins
February 6, 2023
Sarah Tanja
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