Tag Archive

geoduck,

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

NADH dehydrogenase Pgenerosa Identification

  • 2 min read

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)

Read More

Phys Assays Pipeline

  • 6 min read

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

Read More

Back to Top ↑

OA

Metabolic scaling bfactor

  • 1 min read

Objective and summary:


When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.

Read More

Argopecten Qubit 20220608

  • ~1 min read

Objective and summary:


  • DNA extractions of juvenile first generation Bay scalops (F1 A. irradians) extracted 12 indiviauls samples

Read More

Argopecten Qubit 20220131

  • 1 min read

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)

Read More

Daily Wet Lab OA at Point Whitney

  • 12 min read

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.

Read More

Back to Top ↑

scallop,

Hemolymph Bay scallop (testing)

  • 1 min read

Objective:

Bleed a few extra scallops (hatchery in the basement) from the F1 common garden culls ealier this year. Test SYBR green and JC-10 in hemolymph using the protocol written earlier this year with results summarized here

Read More

Argopecten Qubit 20220608

  • ~1 min read

Objective and summary:


  • DNA extractions of juvenile first generation Bay scalops (F1 A. irradians) extracted 12 indiviauls samples

Read More

Argopecten Qubit 20220131

  • 1 min read

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)

Read More

Back to Top ↑

DNA,

Argopecten Qubit 20220608

  • ~1 min read

Objective and summary:


  • DNA extractions of juvenile first generation Bay scalops (F1 A. irradians) extracted 12 indiviauls samples

Read More

F0 Aropecten Qubit 20220110

  • 1 min read

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

Read More

F0 Aropecten Qubit 20220105

  • 1 min read

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

Read More

F0 Argopecten Qubit 20220104

  • ~1 min read

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

Read More

Back to Top ↑

extractions,

Argopecten Qubit 20220608

  • ~1 min read

Objective and summary:


  • DNA extractions of juvenile first generation Bay scalops (F1 A. irradians) extracted 12 indiviauls samples

Read More

Back to Top ↑

zymo,

Back to Top ↑

Qubit,

Argopecten Qubit 20220608

  • ~1 min read

Objective and summary:


  • DNA extractions of juvenile first generation Bay scalops (F1 A. irradians) extracted 12 indiviauls samples

Read More

F0 Aropecten Qubit 20220110

  • 1 min read

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

Read More

F0 Aropecten Qubit 20220105

  • 1 min read

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

Read More

F0 Argopecten Qubit 20220104

  • ~1 min read

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

Read More

Back to Top ↑

NOAA

F0 Aropecten Qubit 20220110

  • 1 min read

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

Read More

F0 Aropecten Qubit 20220105

  • 1 min read

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

Read More

F0 Argopecten Qubit 20220104

  • ~1 min read

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

Read More

Back to Top ↑

RNA,

Back to Top ↑

DNA

Argopecten Qubit 20220131

  • 1 min read

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)

Read More

Back to Top ↑

scallops,

SOP Feeding larvae

  • 6 min read

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.

Read More

Scallop tagging

  • ~1 min read

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)

Read More

F0 Aropecten Qubit 20220110

  • 1 min read

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

Read More

F0 Aropecten Qubit 20220105

  • 1 min read

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

Read More

F0 Argopecten Qubit 20220104

  • ~1 min read

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

Read More

Back to Top ↑

Qubit

Back to Top ↑

dna,

Back to Top ↑

OA,

SOP Feeding larvae

  • 6 min read

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.

Read More

Experiment Prep Point Whitney

  • 1 min read

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.

Read More

Back to Top ↑

extractions

Back to Top ↑

prep,

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

NADH dehydrogenase Pgenerosa Identification

  • 2 min read

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)

Read More

Back to Top ↑

rna

Back to Top ↑

extraction,

Argopecten Qubit 20220131

  • 1 min read

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)

Read More

Back to Top ↑

protocol

Daily Wet Lab OA at Point Whitney

  • 12 min read

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.

Read More

Back to Top ↑

RNA

Back to Top ↑

experiment,

Daily Wet Lab OA at Point Whitney

  • 12 min read

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.

Read More

Daily Wet Lab OA at Point Whitney

  • 12 min read

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.

Read More

Back to Top ↑

qubit,

Argopecten Qubit 20220131

  • 1 min read

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)

Read More

Back to Top ↑

scallop

LISRC Figure

  • ~1 min read

Hello! Thanks for scanning the QR code - review our carbonate chemistry below

Read More

Back to Top ↑

workshop

Back to Top ↑

rna,

Back to Top ↑

tagseq,

Back to Top ↑

gel,

Back to Top ↑

scallops

Back to Top ↑

Illumina,

Back to Top ↑

Rclub

Back to Top ↑

protein,

AOX Pgenerosa identification

  • 2 min read

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)

Read More

Phys Assays Pipeline

  • 6 min read

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

Read More

Back to Top ↑

Geoduck,

Experiment Prep Point Whitney

  • 1 min read

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.

Read More

Back to Top ↑

2020,

Experiment Prep Point Whitney

  • 1 min read

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.

Read More

Back to Top ↑

stress

Experiment Prep Point Whitney

  • 1 min read

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.

Read More

Back to Top ↑

response,

Experiment Prep Point Whitney

  • 1 min read

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.

Read More

Back to Top ↑

hatchery,

Experiment Prep Point Whitney

  • 1 min read

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.

Read More

Back to Top ↑

heathstack,

Experiment Prep Point Whitney

  • 1 min read

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.

Read More

Back to Top ↑

Point

Experiment Prep Point Whitney

  • 1 min read

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.

Read More

Back to Top ↑

Whitney

Experiment Prep Point Whitney

  • 1 min read

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.

Read More

Back to Top ↑

qPCR

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

NADH dehydrogenase Pgenerosa Identification

  • 2 min read

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)

Read More

Back to Top ↑

blasp,

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

NADH dehydrogenase Pgenerosa Identification

  • 2 min read

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)

Read More

Back to Top ↑

blastn,

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

NADH dehydrogenase Pgenerosa Identification

  • 2 min read

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)

Read More

Back to Top ↑

Augustus,

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

NADH dehydrogenase Pgenerosa Identification

  • 2 min read

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)

Read More

Back to Top ↑

Muscle,

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

NADH dehydrogenase Pgenerosa Identification

  • 2 min read

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)

Read More

Back to Top ↑

Pfam,

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

NADH dehydrogenase Pgenerosa Identification

  • 2 min read

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)

Read More

Back to Top ↑

protein

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

NADH dehydrogenase Pgenerosa Identification

  • 2 min read

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)

Read More

Back to Top ↑

design,

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

Back to Top ↑

tagseq

Back to Top ↑

extraction

Back to Top ↑

TA,

Daily Wet Lab OA at Point Whitney

  • 12 min read

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.

Read More

Back to Top ↑

pH,

Daily Wet Lab OA at Point Whitney

  • 12 min read

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.

Read More

Back to Top ↑

APEX,

Daily Wet Lab OA at Point Whitney

  • 12 min read

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.

Read More

Back to Top ↑

sal,

Daily Wet Lab OA at Point Whitney

  • 12 min read

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.

Read More

Back to Top ↑

research,

Daily Wet Lab OA at Point Whitney

  • 12 min read

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.

Read More

Back to Top ↑

HISAT2,

Back to Top ↑

samtools,

Back to Top ↑

StringTie,

Back to Top ↑

fastqc,

Back to Top ↑

multiqc,

Back to Top ↑

fastp

Back to Top ↑

oyster,

Back to Top ↑

omega,

Back to Top ↑

hemolymph

Back to Top ↑

C6_plus

Back to Top ↑

oyster

Back to Top ↑

hemolymph,

Hemolymph Bay scallop (testing)

  • 1 min read

Objective:

Bleed a few extra scallops (hatchery in the basement) from the F1 common garden culls ealier this year. Test SYBR green and JC-10 in hemolymph using the protocol written earlier this year with results summarized here

Read More

Back to Top ↑

flow

Hemolymph Bay scallop (testing)

  • 1 min read

Objective:

Bleed a few extra scallops (hatchery in the basement) from the F1 common garden culls ealier this year. Test SYBR green and JC-10 in hemolymph using the protocol written earlier this year with results summarized here

Read More

Back to Top ↑

library

Back to Top ↑

growth,

Scallop tagging

  • ~1 min read

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)

Read More

Back to Top ↑

Milford

Scallop tagging

  • ~1 min read

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)

Read More

Back to Top ↑

respiration

Metabolic scaling bfactor

  • 1 min read

Objective and summary:


When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.

Read More

Back to Top ↑

metabolism

Metabolic scaling bfactor

  • 1 min read

Objective and summary:


When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.

Read More

Back to Top ↑

R

Back to Top ↑

markdown

Back to Top ↑

workflow

Back to Top ↑

pipeline

Back to Top ↑

bash

Back to Top ↑

physiology,

Phys Assays Pipeline

  • 6 min read

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

Read More

Back to Top ↑

total

Phys Assays Pipeline

  • 6 min read

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

Read More

Back to Top ↑

antioxidant

Phys Assays Pipeline

  • 6 min read

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

Read More

Back to Top ↑

capacity

Phys Assays Pipeline

  • 6 min read

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

Read More

Back to Top ↑

qPCR,

AOX Pgenerosa identification

  • 2 min read

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)

Read More

Back to Top ↑

genome,

AOX Pgenerosa identification

  • 2 min read

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)

Read More

Back to Top ↑

augustus,

AOX Pgenerosa identification

  • 2 min read

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)

Read More

Back to Top ↑

blastp,

AOX Pgenerosa identification

  • 2 min read

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)

Read More

Back to Top ↑

jalview

AOX Pgenerosa identification

  • 2 min read

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)

Read More

Back to Top ↑

primer,

Primer Design

  • 8 min read

Read.me

The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.

Read More

Back to Top ↑

geoduck

Back to Top ↑

proteins

Back to Top ↑

blast

Back to Top ↑

histology

Back to Top ↑

overview,

Back to Top ↑

coral,

Back to Top ↑

porites,

Back to Top ↑

lab

Back to Top ↑

meeting,

Back to Top ↑

trininty,

Back to Top ↑

trinotate,

Back to Top ↑

busco

Back to Top ↑

metabolomics,

Back to Top ↑

Rutgers,

Back to Top ↑

metabolomics

Back to Top ↑

ANOVA,

Back to Top ↑

histology,

Back to Top ↑

gonad,

Back to Top ↑

gametogenesis

Back to Top ↑

extrations,

Back to Top ↑

tem,

Daily Wet Lab OA at Point Whitney

  • 12 min read

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.

Read More

Back to Top ↑

dna,rna

Back to Top ↑

zymop,

Back to Top ↑

qc,

Back to Top ↑

dyna,

Back to Top ↑

repeated

Back to Top ↑

ut,

Back to Top ↑

library,

Back to Top ↑

quality,

Back to Top ↑

temperature,

Back to Top ↑

O2

Back to Top ↑

sensor,

Back to Top ↑

dissolved

Back to Top ↑

oxygen,

Back to Top ↑

Tagseq,

Back to Top ↑

fastp,

Back to Top ↑

mutliqc,

Back to Top ↑

trimming,

Back to Top ↑

polyA

Back to Top ↑

tail,

Back to Top ↑

low

Back to Top ↑

complexity

Back to Top ↑

filtering

Back to Top ↑

DESeq2,

Back to Top ↑

TagSeq,

Back to Top ↑

mRNA,

Back to Top ↑

differential

Back to Top ↑

expression,

Back to Top ↑

stats,

Back to Top ↑

model

Back to Top ↑

multivariate

Back to Top ↑

NOAA,

Back to Top ↑

postdoc

Back to Top ↑

gels,

Back to Top ↑

electrophoresis,

Back to Top ↑

lab,

Back to Top ↑

benchtop

Back to Top ↑

JC-10

Back to Top ↑

DCFHDA

Back to Top ↑

SYBR_green

Back to Top ↑

Extractions,

Back to Top ↑

crassostrea,

Back to Top ↑

cytometry,

Back to Top ↑

C6

Back to Top ↑

plus,

Back to Top ↑

BD

Back to Top ↑

biosciences

Back to Top ↑

Crassostrea

Back to Top ↑

flow_cytometry,

Back to Top ↑

library_prep

Back to Top ↑

Illumina

Back to Top ↑

gel_electrophoresis

Back to Top ↑

common

Scallop tagging

  • ~1 min read

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)

Read More

Back to Top ↑

garden,

Scallop tagging

  • ~1 min read

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)

Read More

Back to Top ↑

raw

Back to Top ↑

data,

Back to Top ↑

basespace,

Back to Top ↑

command

Back to Top ↑

line,

Back to Top ↑

spawners

Back to Top ↑

RShiny,

RShiny calculator app (algae feed)

  • 3 min read

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

Read More

Back to Top ↑

application,

RShiny calculator app (algae feed)

  • 3 min read

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

Read More

Back to Top ↑

algae,

RShiny calculator app (algae feed)

  • 3 min read

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

Read More

Back to Top ↑

efficiency,

RShiny calculator app (algae feed)

  • 3 min read

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

Read More

Back to Top ↑

R,

RShiny calculator app (algae feed)

  • 3 min read

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

Read More

Back to Top ↑

Milford,

SOP Feeding larvae

  • 6 min read

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.

Read More

Back to Top ↑

feed,

SOP Feeding larvae

  • 6 min read

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.

Read More

Back to Top ↑

larvae,

SOP Feeding larvae

  • 6 min read

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.

Read More

Back to Top ↑

static

SOP Feeding larvae

  • 6 min read

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.

Read More

Back to Top ↑

JC10,

Hemolymph Bay scallop (testing)

  • 1 min read

Objective:

Bleed a few extra scallops (hatchery in the basement) from the F1 common garden culls ealier this year. Test SYBR green and JC-10 in hemolymph using the protocol written earlier this year with results summarized here

Read More

Back to Top ↑

bay

Hemolymph Bay scallop (testing)

  • 1 min read

Objective:

Bleed a few extra scallops (hatchery in the basement) from the F1 common garden culls ealier this year. Test SYBR green and JC-10 in hemolymph using the protocol written earlier this year with results summarized here

Read More

Back to Top ↑

SYBR

Hemolymph Bay scallop (testing)

  • 1 min read

Objective:

Bleed a few extra scallops (hatchery in the basement) from the F1 common garden culls ealier this year. Test SYBR green and JC-10 in hemolymph using the protocol written earlier this year with results summarized here

Read More

Back to Top ↑

green,

Hemolymph Bay scallop (testing)

  • 1 min read

Objective:

Bleed a few extra scallops (hatchery in the basement) from the F1 common garden culls ealier this year. Test SYBR green and JC-10 in hemolymph using the protocol written earlier this year with results summarized here

Read More

Back to Top ↑

gating,

Hemolymph Bay scallop (testing)

  • 1 min read

Objective:

Bleed a few extra scallops (hatchery in the basement) from the F1 common garden culls ealier this year. Test SYBR green and JC-10 in hemolymph using the protocol written earlier this year with results summarized here

Read More

Back to Top ↑

cytometry

Hemolymph Bay scallop (testing)

  • 1 min read

Objective:

Bleed a few extra scallops (hatchery in the basement) from the F1 common garden culls ealier this year. Test SYBR green and JC-10 in hemolymph using the protocol written earlier this year with results summarized here

Read More

Back to Top ↑

bfactor

Metabolic scaling bfactor

  • 1 min read

Objective and summary:


When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.

Read More

Back to Top ↑

scaling

Metabolic scaling bfactor

  • 1 min read

Objective and summary:


When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.

Read More

Back to Top ↑

citation

Back to Top ↑

zenodo

Back to Top ↑

Rmarkdown

Back to Top ↑

git

Back to Top ↑

github

Back to Top ↑

RClub

Back to Top ↑

Presens

Back to Top ↑

Loligo

Back to Top ↑

lcWGS

Back to Top ↑

if

Back to Top ↑

else

Back to Top ↑

boolean

Back to Top ↑

forloop

Back to Top ↑

aquaculture,

Back to Top ↑

handbook,

Back to Top ↑

priming

Back to Top ↑

figure

LISRC Figure

  • ~1 min read

Hello! Thanks for scanning the QR code - review our carbonate chemistry below

Read More

Back to Top ↑

QRcode

LISRC Figure

  • ~1 min read

Hello! Thanks for scanning the QR code - review our carbonate chemistry below

Read More

Back to Top ↑

acidification

LISRC Figure

  • ~1 min read

Hello! Thanks for scanning the QR code - review our carbonate chemistry below

Read More

Back to Top ↑

pCO2

LISRC Figure

  • ~1 min read

Hello! Thanks for scanning the QR code - review our carbonate chemistry below

Read More

Back to Top ↑

popgen

Back to Top ↑

genomics

Back to Top ↑

angsd

Back to Top ↑

snp_calling

Back to Top ↑

clusters

Back to Top ↑

bioinformatics

Back to Top ↑

snakemake

Back to Top ↑

computing

Back to Top ↑

python

Back to Top ↑

cluster

Back to Top ↑