Posts

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Backup your work

using rsync
code
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…
Nov 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??
Oct 8, 2024
Sarah Tanja
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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…
Oct 8, 2024
Sarah Tanja
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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…
Oct 7, 2024
Sarah Tanja
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Summary of previous research on microplastic leachate exposure in marine invertebrate embryonic development

In sea urchin and mussel model organisms
learning journey
coral
PVC pellet leachates affect adult immune system and embryonic development but not reproductive capacity in the sea urchin Paracentrotus lividus
Oct 7, 2024
Sarah Tanja

Ontogenetic Development of Montipora capitata

learning journey
coral
Montipora capitata cora…
Sep 30, 2024
Sarah Tanja
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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.
Sep 9, 2024
Sarah Tanja
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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 illustrate the categories of embryonic development in Montipora capitata that we are characterizing in this study:
Sep 9, 2024
Sarah Tanja
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Timeline & Goals Planning

committee
goals
This is a timeline of goals and progress made toward wrapping up my Master’s Thesis at UW SAFS.
Sep 8, 2024
Sarah Tanja
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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)? This experiment allowed embryos to develop from a bundle-bundle…
Sep 6, 2024
Sarah Tanja
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Nikon scope pictures & slide preservation protocol

For capturing embryonic development of Montipora capitata rice corals exposed to PVC leachate
protocols
coral
Watch ’Mounting Your Specimen’ by Dr. Terry Bruce on YouTube
Sep 3, 2024
Sarah Tanja
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26-Aug-2024 Embryo RNA Extractions

lab records
8C9F, 9C9F = 89C91
Aug 26, 2024
Sarah Tanja
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23-Aug-2024 Embryo RNA Extractions

lab records
4L14F, 5CL14F, 6L14HF = 456L14
Aug 23, 2024
Sarah Tanja
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21-Aug-2024 Embryo RNA Extractions

lab records
1C14F, 2C14F, 3C14HF = 123C14
Aug 21, 2024
Sarah Tanja
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20-Aug-2024 Embryo RNA Extractions

lab records
1H9F, 2H9F, 3H9F = 123H9
Aug 20, 2024
Sarah Tanja
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19-Aug-2024 Embryo RNA Extractions

lab records
4H9F, 5H9F, 6H9F = 456H9
Aug 19, 2024
Sarah Tanja
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16-Aug-2024 Embryo RNA Extractions

lab records
1L4F, 2L4F, 3L4F = 123L4
Aug 16, 2024
Sarah Tanja
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15-Aug-2024 Embryo RNA Extractions

lab records
4C14F, 5C14F = 45C14
Aug 15, 2024
Sarah Tanja
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14-Aug-2024 Embryo RNA Extractions

lab records
1C4F, 2C4F, 3C4F = 123C4
Aug 14, 2024
Sarah Tanja
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13-Aug-2024 Embryo RNA Extractions

lab records
coral
1C9F, 2C9F, 3C9F = 123C9F
Aug 13, 2024
Sarah Tanja
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12-Aug-2024 Embryo RNA Extractions

lab records
6C14F (single sample ~10 embryos)
Aug 12, 2024
Sarah Tanja
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M. Capitata Embryo DNA/RNA Extractions Protocol

protocols
coral
For inspiration checkout:
Aug 9, 2024
Sarah Tanja
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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…
Jul 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
Jul 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…
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 Anthop…
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 to their diet, or…
May 2, 2024
Sarah Tanja

Anemone Leachate Heat Experiment Recipe

anemones
protocols
Collect anemones
Apr 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!
Apr 22, 2024
Sarah Tanja

Puget Sound Microplastics

learning journey
What are the…
Apr 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 permit Tanja 24-010. At this site we collected 10 anemones from each of 4…
Mar 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 his lab of environmental chemists…
Mar 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 Tanja…
Mar 18, 2024
Sarah Tanja
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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
Feb 22, 2024
Sarah Tanja

Experimental tank setup

protocols
anemones
Hydra 32HD manual
Feb 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…
Feb 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…
Feb 5, 2024
Sarah Tanja

Anemone Project Planning

anemones
The objective of this study is to…
Jan 2, 2024
Sarah Tanja

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

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

Pseudoreplication & Control

How to design a manipulation experiment
learning journey
“the use of inferential…
Dec 6, 2023
Sarah Tanja

Phthalates around the World

learning journey
What are the common…
Nov 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
Nov 19, 2023
Sarah Tanja

Master’s Thesis Progress

learning journey
committee
SAFS Masters Thesis Milestones are laid out here
Nov 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 \(…
Nov 14, 2023
Sarah Tanja

Git Reset

For all the times I accidentally commit a file that is too big
code
In this assignment we’re dealing with large files that will end up in the ../data and ../output directories. To prevent those large files from…
Nov 5, 2023
Sarah Tanja

Dual DNA & RNA Extraction Protocol

protocols
The aim of this protocol is to take coral fragments that have been snap-frozen in…
Aug 23, 2023
Sarah Tanja

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:
Aug 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…
Aug 10, 2023
Sarah Tanja

Target Journals for Submitting Manuscripts

learning journey
Impact Factor 8.9
Jul 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…
Jun 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 compare two bead-beating methods so the differences…
Jun 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

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.
Apr 25, 2023
Sarah Tanja

Master’s Thesis Committee Meeting #1

committee
Introduction - 5 mins
Feb 6, 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.
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Sarah Tanja
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