Posts
snakemake tips
popgen workflow
Pogen workflow
LISRC Figure
Hello! Thanks for scanning the QR code - review our carbonate chemistry below
Geoduck handbook
For loop workshop
For. Loop. Fun.
Boolean workshop
If / Else Workshop
Airradians lcWGS HPC pipeline
Table of Contents
- Upon upload to HPC…
- Digital fingerprint md5sums (HPC script; md5_checksum.sh)
- 1. MultiQC: Initial QC (HPC script; mutliqc.sh)
- 2. Trimming and QC of ‘clean’ reads
- fastp - about/commands
- fastp and MulitiQC: Trim and QC (HPC script; fastp_mutliqc.sh)
- 3. Alignment of cleaned reads to reference
- Upload reference genome
- HISAT2 - about/commands
- samtools - about/commands
- HISAT2: Index reference and alignment (HPC script; HISAT2.sh)
Github workshop
Metabolic rate workflow
Metabolic rate workflow
Time to git started
How to set up citation in R markdowns
Obj: Link citations within R markdown text for project files and manuscripts
Metabolic scaling bfactor
Objective and summary:
When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.
Hemolymph Bay scallop (testing)
Illumina DNA Prep with KAPA and Ampure SOP
Illumina DNA Prep with TD, TDE, KAPA and Ampure SOP
F1 Argopecten Qubit 20220912
Objective and summary:
SOP Feeding larvae
SOP! Feeding larvae in static system
Objective:
Batch feed larvae using all precautions necessary for a static system (1) assess the current algal density of both the culture and static larval system using flow cytometry (2) add the correct volume of algae to a target cell density.
RShiny calculator app (algae feed)
How to build an RShiny - algae feed calculator:
Showcase an simple example of an RShiny built for calculating the volume of known algae culture for feeding bivalve larvae
F1 Broodstock spawners tagged
Download Illumina seq data to personal computer (using cmd line)
Illumina Basespace –> personal computer (using cmd line):
How to download FASTQ files from basespace through the command line
Scallop tagging
Objective and summary:
- Measure and tag all Bay scallops in the minnow cool systems. There are
two sets of scallops that have been reared under raw water common garden from the 8 and 7.5 pH conditions.
- March 6th (‘old’ group)
- April 26th (‘new’ group)
F1 Argopecten Gel 20220616
Objective and summary:
- Run ethidium bromide gel electrophoresis for post-library prep samples F1 Juvenile Bay Scallop 8C 101 and 102
Argopecten Qubit 20220608
Objective and summary:
- DNA extractions of juvenile first generation Bay scalops (F1 A. irradians) extracted 12 indiviauls samples
F1 Argopecten Gel 20220607
Objective and summary:
- Run ethidium bromide gel electrophoresis for post-library prep samples F1 Juvenile Bay SCallop 8B 51 and 8B 52
Oyster hemolymph flow cytometry cont..
F1 Argopecten Gel 20220606
Illumina DNA Prep with KAPA and Ampure SOP
Illumina DNA Prep with KAPA and Ampure SOP
Illumina DNA Prep SOP
Illumina DNA Prep SOP
Argopecten Qubit 20220602
Objective and summary:
Argopecten Qubit 20220531
Objective and summary:
Argopecten Qubit 20220407
Objective and summary:
Argopecten Qubit 20220406
Argopecten Qubit 20220331
Argopecten Qubit 20220323
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
Argopecten Qubit 202200309
Hemolymph physiology flow cytometry protocol
Argopecten Qubit 20220308
Objective and summary:
Argopecten Qubit 20220207
Objective and summary:
Argopecten Qubit 20220131
Objective and summary:
-
Complete extraction and qubit quantification using non-target adult scallop samples
- 30 mg and 90 mg of tissue
- 3 hr Proteinase K incubation at 120 RPM and 55C - vortexed every hour
- doubled the volume of TL Buffer, HBC buffer and 100% ethanol for the 60 mg samples (did not double proteinase K)
F0 Argopecten Gel 20220118
Gel Electrophoresis with ethidium bromide
Gel electrophoresis (ethidium bromide)
Note: this protocol if you are imaging a gel today, turn on the computer for the GenSys software (computer takes a while to boot up)
F0 Aropecten Qubit 20220110
Objective and summary:
- Measure DNA concentrations of DNA extracted from F0 adult Bay scallop adductor tissue (dissected and extracted in early January 2022)
- DNA was extracted using the OMEGA EZNA Tissue kit protocol here
- Ran Qubit dsDNA BR kit following standard protocol thermosci online pdf
F0 Aropecten Qubit 20220105
Objective and summary:
- Measure DNA concentrations of DNA extracted from F0 adult Bay scallop adductor tissue (dissected and extracted in early January 2022)
- DNA was extracted using the OMEGA EZNA Tissue kit protocol here
- Ran Qubit dsDNA BR kit following standard protocol thermosci online pdf
F0 Argopecten Qubit 20220104
Objective and summary:
- Measure DNA concentrations of DNA extracted from F0 adult Bay scallop adductor tissue (dissected and extracted in late December 2021)
- DNA was extracted using the OMEGA EZNA Tissue kit protocol here
- Ran Qubit dsDNA BR kit following standard protocol thermosci online pdf
Airradians adult DNA extractions
…the following protocol is adapted from the OMEGA EZNA Tissiue kit online here
Pgenerosa_tagseq_wgcna_results
layout: post title: Pgenerosa_TagSeq_WGCNa_Results date: ‘2021-03-18’ categories: Analysis tags: pgenerosa, tagseq, WGCNA, RNAseq, gene expression, oxidative stress, hormetic priming —
First a review of our phenotype and experimental design…
Self_assessment_plan
Sam Gurr
2021 Self-Assessment
Goals this year 2021
layout: post title: Self_Assessment_Plan date: ‘2021-03-12’ categories: Processing tags: Self, Goals —
Multivariate Analysis DESeq2
Tips on multivariate analysis in DESeq2
An odd case of %GC
TagSeq QC troubleshooting
Oyster TagSeq Pipeline
Oyster (Crassostrea virgninca) TagSeq Bioinformatics
O2 sensor protocol Hach HQ30d
last updated 20210107
Geoduck TagSeq Pipeline
Geoduck TagSeq Bioinformatics
URI GSO Water Quality
last update SJG 20200105
TagSeq UT Library QC
TagSeq UT Library QC
REPEATED QC 20201001 Juvenile Panpoea generosa Extractions
Objective:
20200923 Juvenile Panopea generosa DNA RNA Extractions
Objective:
20200917 Juvenile Panopea generosa DNA RNA Extractions
Objective:
20200910 Juvenile Panopea generosa DNA RNA Extractions
Objective:
20200909 Juvenile Panopea generosa DNA RNA Extractions
Daily Wet Lab OA at Point Whitney
Point Whitney Hatchery and Lab Information
Last Revised: 20181030 SJ Gurr
Lab Need to Know:
- Dry bench (1st bench, closest to light set switches) should stay dry, do not move wet/liquid materials since electronics including laptops are kept here.
20200903 Juvenile Panopea generosa DNa RNA Extractions
20200827 Juvenile Panopea generosa DNA RNA Extractions
20200826 Juvenile Panopea generosa DNA RNA Extractions
20200825 Juvenile Panopea generosa DNa RNA Extractions
20200824 Juvenile Panopea generosa DNA RNA Extractions
Pgenerosa_male_histology_results
P. generosa Male Histology Results
Updated protocol - DNA RNA Extraction of geoduck samples (Zymo kit)
PROTOCOL: DNA/RNA Extractions of P. generosa samples
20200817 20200818 Juvenile Panopea generosa DNA RNA extractions
2020-08-12-Geoduck-metabolomics-extraction
Objective(s):
- Prepare geoduck metabolomic samples for analysis following the follwoing links:
- Six samples were prepped on 8/11/20 for 1 animal and 4 animals in triplicate view table here - today I will prep three additional samples with 7 animals each final table at the end of this post
Geoduck metabolomics extraction
Metabolomics of juvenile P. generosa - Sample preparation
Geoduck DNA RNA extraction
Geoduck DNA/RNA extractions
202007-Lab Meeting; Porites astreoides assembly
Porites astreoides transcriptome assembly
Gonad_Histology
Pacific geoduck gonad histology analysis (Image J)
TagSeq_prep_Pgenerosa_putative_genes
Summary of Experiment in 2019
Primer Design
Read.me
The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.
NADH dehydrogenase Pgenerosa Identification
OBJECTIVE
The following protocol was completed with the geoduck genome in preparation for primer design and qPCR of a target protein NADH dehydrogenase (complex I) This step-by-step process can be used to verify the presence/absence of a particular target gene within an annotated genome without gene family identification. In this case.. a database of the geoduck genome was used with only ID identifiers for genes (no family-specific accession ID)
Experiment Prep Point Whitney
read.me
The following is a summary of a trip to Jamestown Point Whitney Shellfish Hatchery in Brinnon, Washingston frmo 3/6/20 - 3/13/20.
2020-03-12_8_month_OA_Experiment_Plan
AOX Pgenerosa identification
OBJECTIVE
The following protocol was completed with the geoduck genome in preparation for primer design and qPCR of a target protein Alternative oxidase This step-by-step process can be used to verify the presence/absence of a particular target gene within an annotated genome without gene family identification. In this case.. a database of the geoduck genome was used with only ID identifiers for genes (no family-specific accession ID)
pCO2 Thresholds Experiment
Image upload practice This is a first attempt to link an image to a github online notebook!
Phys Assays Pipeline
Pipeline for geoduck physiology (oxidative stress, total protein, & AFDW/condition index)
NOTE: the following protocol was followed in analysis of juvenile geoduck (~5-8mm shell length) from an OA experiment completed in summer 2019. Juvenile geoduck (whole animals) were snap frozen in LN2 at the hatcheryand stored at -80°C until later analysis