- geoduck, 22
- OA 15
- scallop, 15
- DNA, 14
- extractions, 13
- zymo, 10
- Qubit, 10
- NOAA 9
- RNA, 8
- DNA 8
- scallops, 7
- Qubit 7
- dna, 6
- OA, 5
- extractions 5
- prep, 4
- rna 4
- extraction, 4
- protocol 4
- RNA 4
- experiment, 4
- qubit, 4
- workshop 4
- rna, 3
- tagseq, 3
- gel, 3
- scallops 3
- scallop 3
- Illumina, 3
- Rclub 3
- protein, 2
- Geoduck, 2
- 2020, 2
- stress 2
- response, 2
- hatchery, 2
- heathstack, 2
- Point 2
- Whitney 2
- qPCR 2
- blasp, 2
- blastn, 2
- Augustus, 2
- Muscle, 2
- Pfam, 2
- protein 2
- design, 2
- tagseq 2
- extraction 2
- TA, 2
- pH, 2
- APEX, 2
- sal, 2
- research, 2
- HISAT2, 2
- samtools, 2
- StringTie, 2
- fastqc, 2
- multiqc, 2
- fastp 2
- oyster, 2
- omega, 2
- hemolymph 2
- C6_plus 2
- oyster 2
- hemolymph, 2
- flow 2
- library 2
- growth, 2
- Milford 2
- respiration 2
- metabolism 2
- R 2
- markdown 2
- physiology, 1
- total 1
- antioxidant 1
- capacity 1
- qPCR, 1
- genome, 1
- augustus, 1
- blastp, 1
- jalview 1
- primer, 1
- geoduck 1
- proteins 1
- blast 1
- histology 1
- overview, 1
- coral, 1
- porites, 1
- lab 1
- meeting, 1
- trininty, 1
- trinotate, 1
- busco 1
- metabolomics, 1
- Rutgers, 1
- metabolomics 1
- ANOVA, 1
- histology, 1
- gonad, 1
- gametogenesis 1
- extrations, 1
- tem, 1
- dna,rna 1
- zymop, 1
- qc, 1
- dyna, 1
- repeated 1
- ut, 1
- library, 1
- quality, 1
- temperature, 1
- O2 1
- sensor, 1
- dissolved 1
- oxygen, 1
- Tagseq, 1
- fastp, 1
- mutliqc, 1
- trimming, 1
- polyA 1
- tail, 1
- low 1
- complexity 1
- filtering 1
- DESeq2, 1
- TagSeq, 1
- mRNA, 1
- differential 1
- expression, 1
- stats, 1
- model 1
- multivariate 1
- NOAA, 1
- postdoc 1
- gels, 1
- electrophoresis, 1
- lab, 1
- benchtop 1
- JC-10 1
- DCFHDA 1
- SYBR_green 1
- Extractions, 1
- crassostrea, 1
- cytometry, 1
- C6 1
- plus, 1
- BD 1
- biosciences 1
- Crassostrea 1
- flow_cytometry, 1
- library_prep 1
- Illumina 1
- gel_electrophoresis 1
- common 1
- garden, 1
- raw 1
- data, 1
- basespace, 1
- command 1
- line, 1
- spawners 1
- RShiny, 1
- application, 1
- algae, 1
- efficiency, 1
- R, 1
- Milford, 1
- feed, 1
- larvae, 1
- static 1
- JC10, 1
- bay 1
- SYBR 1
- green, 1
- gating, 1
- cytometry 1
- bfactor 1
- scaling 1
- citation 1
- zenodo 1
- Rmarkdown 1
- git 1
- github 1
- RClub 1
- Presens 1
- Loligo 1
- lcWGS 1
- workflow 1
- pipeline 1
- if 1
- else 1
- boolean 1
- forloop 1
- aquaculture, 1
- handbook, 1
- priming 1
geoduck,
Geoduck handbook
Geoduck TagSeq Pipeline
Geoduck TagSeq Bioinformatics
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
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
Gonad_Histology
Pacific geoduck gonad histology analysis (Image J)
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)
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
OA
Metabolic scaling bfactor
Objective and summary:
When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.
Illumina DNA Prep with KAPA and Ampure SOP
Illumina DNA Prep with TD, TDE, KAPA and Ampure SOP
Argopecten Qubit 20220608
Objective and summary:
- DNA extractions of juvenile first generation Bay scalops (F1 A. irradians) extracted 12 indiviauls samples
Oyster hemolymph flow cytometry cont..
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 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)
URI GSO Water Quality
last update SJG 20200105
20200923 Juvenile Panopea generosa DNA RNA Extractions
Objective:
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.
scallop,
Hemolymph Bay scallop (testing)
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 20220606
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
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
DNA,
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
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 20220606
Illumina DNA Prep SOP
Illumina DNA Prep SOP
Argopecten Qubit 20220602
Objective and summary:
Argopecten Qubit 20220531
Objective and summary:
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
20200827 Juvenile Panopea generosa DNA RNA Extractions
20200825 Juvenile Panopea generosa DNa RNA Extractions
Geoduck DNA RNA extraction
Geoduck DNA/RNA extractions
extractions,
Argopecten Qubit 20220608
Objective and summary:
- DNA extractions of juvenile first generation Bay scalops (F1 A. irradians) extracted 12 indiviauls samples
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:
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
20200903 Juvenile Panopea generosa DNa RNA Extractions
20200826 Juvenile Panopea generosa DNA RNA Extractions
20200825 Juvenile Panopea generosa DNa RNA Extractions
zymo,
20200923 Juvenile Panopea generosa DNA RNA Extractions
Objective:
20200910 Juvenile Panopea generosa DNA RNA Extractions
Objective:
20200909 Juvenile Panopea generosa DNA RNA Extractions
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
20200817 20200818 Juvenile Panopea generosa DNA RNA extractions
Geoduck DNA RNA extraction
Geoduck DNA/RNA extractions
Qubit,
Argopecten Qubit 20220608
Objective and summary:
- DNA extractions of juvenile first generation Bay scalops (F1 A. irradians) extracted 12 indiviauls samples
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 202200309
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
NOAA
For loop workshop
For. Loop. Fun.
Boolean workshop
If / Else Workshop
Github workshop
Metabolic rate workflow
Metabolic rate workflow
Time to git started
F1 Argopecten Qubit 20220912
Objective and summary:
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
RNA,
Argopecten Qubit 20220407
Objective and summary:
Argopecten Qubit 20220406
Argopecten Qubit 20220331
Argopecten Qubit 20220323
Argopecten Qubit 202200309
Oyster TagSeq Pipeline
Oyster (Crassostrea virgninca) TagSeq Bioinformatics
Geoduck TagSeq Pipeline
Geoduck TagSeq Bioinformatics
Geoduck DNA RNA extraction
Geoduck DNA/RNA extractions
DNA
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:
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
Illumina DNA Prep with KAPA and Ampure SOP
Illumina DNA Prep with KAPA and Ampure SOP
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
scallops,
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.
F1 Broodstock spawners tagged
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)
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
Qubit
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:
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
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
F1 Argopecten Gel 20220606
Illumina DNA Prep with KAPA and Ampure SOP
Illumina DNA Prep with KAPA and Ampure SOP
Argopecten Qubit 20220331
dna,
20200923 Juvenile Panopea generosa DNA RNA Extractions
Objective:
20200917 Juvenile Panopea generosa DNA RNA Extractions
Objective:
20200909 Juvenile Panopea generosa DNA RNA Extractions
20200903 Juvenile Panopea generosa DNa RNA Extractions
20200826 Juvenile Panopea generosa DNA RNA Extractions
20200817 20200818 Juvenile Panopea generosa DNA RNA extractions
OA,
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.
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
Pgenerosa_male_histology_results
P. generosa Male Histology Results
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
extractions
Illumina DNA Prep with KAPA and Ampure SOP
Illumina DNA Prep with TD, TDE, KAPA and Ampure SOP
Illumina DNA Prep with KAPA and Ampure SOP
Illumina DNA Prep with KAPA and Ampure SOP
Argopecten Qubit 20220406
Argopecten Qubit 20220323
20200824 Juvenile Panopea generosa DNA RNA Extractions
prep,
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
F1 Argopecten Gel 20220606
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)
rna
20200909 Juvenile Panopea generosa DNA RNA Extractions
20200903 Juvenile Panopea generosa DNa RNA Extractions
20200826 Juvenile Panopea generosa DNA RNA Extractions
20200817 20200818 Juvenile Panopea generosa DNA RNA extractions
extraction,
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)
Updated protocol - DNA RNA Extraction of geoduck samples (Zymo kit)
PROTOCOL: DNA/RNA Extractions of P. generosa samples
protocol
O2 sensor protocol Hach HQ30d
last updated 20210107
URI GSO Water Quality
last update SJG 20200105
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.
Updated protocol - DNA RNA Extraction of geoduck samples (Zymo kit)
PROTOCOL: DNA/RNA Extractions of P. generosa samples
RNA
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
TagSeq UT Library QC
TagSeq UT Library QC
20200827 Juvenile Panopea generosa DNA RNA Extractions
20200825 Juvenile Panopea generosa DNa RNA Extractions
experiment,
URI GSO Water Quality
last update SJG 20200105
URI GSO Water Quality
last update SJG 20200105
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.
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.
qubit,
Argopecten Qubit 20220323
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)
workshop
For loop workshop
For. Loop. Fun.
Boolean workshop
If / Else Workshop
Github workshop
Time to git started
rna,
REPEATED QC 20201001 Juvenile Panpoea generosa Extractions
Objective:
20200923 Juvenile Panopea generosa DNA RNA Extractions
Objective:
20200917 Juvenile Panopea generosa DNA RNA Extractions
Objective:
gel,
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
F1 Argopecten Gel 20220606
F0 Argopecten Gel 20220118
scallops
Metabolic rate workflow
Metabolic rate workflow
F1 Argopecten Qubit 20220912
Objective and summary:
Argopecten Qubit 202200309
scallop
Illumina DNA Prep with KAPA and Ampure SOP
Illumina DNA Prep with TD, TDE, KAPA and Ampure SOP
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
Illumina DNA Prep with KAPA and Ampure SOP
Illumina DNA Prep with KAPA and Ampure SOP
Illumina,
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
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
F1 Argopecten Gel 20220606
Rclub
Back to Top ↑protein,
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)
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
Geoduck,
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
2020,
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
stress
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
response,
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
hatchery,
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
heathstack,
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
Point
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
Whitney
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
qPCR
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)
blasp,
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)
blastn,
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)
Augustus,
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)
Muscle,
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)
Pfam,
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)
protein
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)
design,
Multivariate Analysis DESeq2
Tips on multivariate analysis in DESeq2
Primer Design
Read.me
The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.
extraction
Geoduck metabolomics extraction
Metabolomics of juvenile P. generosa - Sample preparation
Geoduck DNA RNA extraction
Geoduck DNA/RNA extractions
TA,
URI GSO Water Quality
last update SJG 20200105
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.
pH,
URI GSO Water Quality
last update SJG 20200105
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.
APEX,
URI GSO Water Quality
last update SJG 20200105
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.
sal,
URI GSO Water Quality
last update SJG 20200105
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.
research,
URI GSO Water Quality
last update SJG 20200105
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.
HISAT2,
Oyster TagSeq Pipeline
Oyster (Crassostrea virgninca) TagSeq Bioinformatics
Geoduck TagSeq Pipeline
Geoduck TagSeq Bioinformatics
samtools,
Oyster TagSeq Pipeline
Oyster (Crassostrea virgninca) TagSeq Bioinformatics
Geoduck TagSeq Pipeline
Geoduck TagSeq Bioinformatics
StringTie,
Oyster TagSeq Pipeline
Oyster (Crassostrea virgninca) TagSeq Bioinformatics
Geoduck TagSeq Pipeline
Geoduck TagSeq Bioinformatics
fastqc,
Oyster TagSeq Pipeline
Oyster (Crassostrea virgninca) TagSeq Bioinformatics
Geoduck TagSeq Pipeline
Geoduck TagSeq Bioinformatics
multiqc,
Oyster TagSeq Pipeline
Oyster (Crassostrea virgninca) TagSeq Bioinformatics
Geoduck TagSeq Pipeline
Geoduck TagSeq Bioinformatics
fastp
Oyster TagSeq Pipeline
Oyster (Crassostrea virgninca) TagSeq Bioinformatics
Geoduck TagSeq Pipeline
Geoduck TagSeq Bioinformatics
oyster,
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
Oyster TagSeq Pipeline
Oyster (Crassostrea virgninca) TagSeq Bioinformatics
omega,
Argopecten Qubit 20220308
Objective and summary:
Argopecten Qubit 20220207
Objective and summary:
hemolymph
Back to Top ↑C6_plus
Back to Top ↑oyster
Back to Top ↑hemolymph,
Hemolymph Bay scallop (testing)
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
flow
Hemolymph Bay scallop (testing)
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
library
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
F1 Argopecten Gel 20220606
growth,
F1 Broodstock spawners tagged
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)
Milford
F1 Broodstock spawners tagged
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)
respiration
Metabolic rate workflow
Metabolic rate workflow
Metabolic scaling bfactor
Objective and summary:
When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.
metabolism
Metabolic rate workflow
Metabolic rate workflow
Metabolic scaling bfactor
Objective and summary:
When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.
R
For loop workshop
For. Loop. Fun.
Metabolic rate workflow
Metabolic rate workflow
markdown
Airradians lcWGS HPC pipeline
Table of Contents
- Upon upload to HPC…
- 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
physiology,
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
total
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
antioxidant
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
capacity
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
qPCR,
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)
genome,
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)
augustus,
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)
blastp,
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)
jalview
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)
primer,
Primer Design
Read.me
The following is a condensed summary of computational work from blast gene identification to primer testing in preparation for qPCR.
geoduck
TagSeq_prep_Pgenerosa_putative_genes
Summary of Experiment in 2019
proteins
TagSeq_prep_Pgenerosa_putative_genes
Summary of Experiment in 2019
blast
TagSeq_prep_Pgenerosa_putative_genes
Summary of Experiment in 2019
histology
Gonad_Histology
Pacific geoduck gonad histology analysis (Image J)
overview,
202007-Lab Meeting; Porites astreoides assembly
Porites astreoides transcriptome assembly
coral,
202007-Lab Meeting; Porites astreoides assembly
Porites astreoides transcriptome assembly
porites,
202007-Lab Meeting; Porites astreoides assembly
Porites astreoides transcriptome assembly
lab
202007-Lab Meeting; Porites astreoides assembly
Porites astreoides transcriptome assembly
meeting,
202007-Lab Meeting; Porites astreoides assembly
Porites astreoides transcriptome assembly
trininty,
202007-Lab Meeting; Porites astreoides assembly
Porites astreoides transcriptome assembly
trinotate,
202007-Lab Meeting; Porites astreoides assembly
Porites astreoides transcriptome assembly
busco
202007-Lab Meeting; Porites astreoides assembly
Porites astreoides transcriptome assembly
metabolomics,
Geoduck metabolomics extraction
Metabolomics of juvenile P. generosa - Sample preparation
Rutgers,
Geoduck metabolomics extraction
Metabolomics of juvenile P. generosa - Sample preparation
metabolomics
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
ANOVA,
Pgenerosa_male_histology_results
P. generosa Male Histology Results
histology,
Pgenerosa_male_histology_results
P. generosa Male Histology Results
gonad,
Pgenerosa_male_histology_results
P. generosa Male Histology Results
gametogenesis
Pgenerosa_male_histology_results
P. generosa Male Histology Results
extrations,
Back to Top ↑tem,
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.
dna,rna
Back to Top ↑zymop,
Back to Top ↑qc,
Back to Top ↑dyna,
Back to Top ↑repeated
Back to Top ↑ut,
TagSeq UT Library QC
TagSeq UT Library QC
library,
TagSeq UT Library QC
TagSeq UT Library QC
quality,
TagSeq UT Library QC
TagSeq UT Library QC
temperature,
URI GSO Water Quality
last update SJG 20200105
O2
O2 sensor protocol Hach HQ30d
last updated 20210107
sensor,
O2 sensor protocol Hach HQ30d
last updated 20210107
dissolved
O2 sensor protocol Hach HQ30d
last updated 20210107
oxygen,
O2 sensor protocol Hach HQ30d
last updated 20210107
fastp,
An odd case of %GC
TagSeq QC troubleshooting
mutliqc,
An odd case of %GC
TagSeq QC troubleshooting
trimming,
An odd case of %GC
TagSeq QC troubleshooting
polyA
An odd case of %GC
TagSeq QC troubleshooting
tail,
An odd case of %GC
TagSeq QC troubleshooting
low
An odd case of %GC
TagSeq QC troubleshooting
complexity
An odd case of %GC
TagSeq QC troubleshooting
filtering
An odd case of %GC
TagSeq QC troubleshooting
DESeq2,
Multivariate Analysis DESeq2
Tips on multivariate analysis in DESeq2
mRNA,
Multivariate Analysis DESeq2
Tips on multivariate analysis in DESeq2
differential
Multivariate Analysis DESeq2
Tips on multivariate analysis in DESeq2
expression,
Multivariate Analysis DESeq2
Tips on multivariate analysis in DESeq2
stats,
Multivariate Analysis DESeq2
Tips on multivariate analysis in DESeq2
model
Multivariate Analysis DESeq2
Tips on multivariate analysis in DESeq2
multivariate
Multivariate Analysis DESeq2
Tips on multivariate analysis in DESeq2
NOAA,
Airradians adult DNA extractions
…the following protocol is adapted from the OMEGA EZNA Tissiue kit online here
postdoc
Airradians adult DNA extractions
…the following protocol is adapted from the OMEGA EZNA Tissiue kit online here
gels,
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)
electrophoresis,
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)
lab,
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)
benchtop
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)
JC-10
Back to Top ↑DCFHDA
Back to Top ↑SYBR_green
Back to Top ↑Extractions,
Back to Top ↑crassostrea,
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
cytometry,
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
C6
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
plus,
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
BD
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
biosciences
Oyster hemolymph flow cytometry
Flow Cytometry for Oyster (Crassostrea virginica) Hemolymph
Last Revised: 20220324 SJ Gurr
Crassostrea
Back to Top ↑flow_cytometry,
Back to Top ↑library_prep
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
Illumina
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
gel_electrophoresis
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
common
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)
garden,
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)
raw
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
data,
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
basespace,
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
command
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
line,
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
spawners
Back to Top ↑RShiny,
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
application,
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
algae,
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
efficiency,
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
R,
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
Milford,
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.
feed,
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.
larvae,
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.
static
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.
JC10,
Back to Top ↑bay
Back to Top ↑SYBR
Back to Top ↑green,
Back to Top ↑gating,
Back to Top ↑cytometry
Back to Top ↑bfactor
Metabolic scaling bfactor
Objective and summary:
When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.
scaling
Metabolic scaling bfactor
Objective and summary:
When possible, it is critical to normalize physiological rates allometrically, as they are often proportional to boy mass.
citation
How to set up citation in R markdowns
Obj: Link citations within R markdown text for project files and manuscripts
zenodo
How to set up citation in R markdowns
Obj: Link citations within R markdown text for project files and manuscripts
Rmarkdown
How to set up citation in R markdowns
Obj: Link citations within R markdown text for project files and manuscripts
git
Back to Top ↑github
Back to Top ↑RClub
Back to Top ↑Presens
Metabolic rate workflow
Metabolic rate workflow
Loligo
Metabolic rate workflow
Metabolic rate workflow
lcWGS
Airradians lcWGS HPC pipeline
Table of Contents
- Upon upload to HPC…
- 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)
workflow
Airradians lcWGS HPC pipeline
Table of Contents
- Upon upload to HPC…
- 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)
pipeline
Airradians lcWGS HPC pipeline
Table of Contents
- Upon upload to HPC…
- 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)