http://lod.bco-dmo.org/id/dataset/958359
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2025-04-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Restriction site-associated DNA sequence metadata of Kelletia kelletii collected in California, USA and Baja, Mexico in 2015 to 2017
2025-04-09
publication
2025-04-09
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-04-10
publication
https://doi.org/10.26008/1912/bco-dmo.958359.1
Robert J. Toonen
University of Hawaiʻi at Mānoa
principalInvestigator
Crow White
Cal Poly San Luis Obispo
principalInvestigator
Mark Christie
Purdue University
principalInvestigator
Benjamin Daniels
Oregon State University
principalInvestigator
Jean Davidson
Cal Poly San Luis Obispo
principalInvestigator
Freel Evan
University of Hawaiʻi at Mānoa
principalInvestigator
Andy Lee
Purdue University
principalInvestigator
Cataixa López
University of Hawaiʻi at Mānoa
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: White, C., Christie, M., Toonen, R. J., López, C., Lee, A., Davidson, J., Daniels, B., Evan, F. (2025) Restriction site-associated DNA sequence metadata of Kelletia kelletii collected in California, USA and Baja, Mexico in 2015 to 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-04-09 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.958359.1 [access date]
Kelletia kelletii Pooled RADseq Dataset Description: Methods and Sampling: <p><em>Sample collection, DNA extraction, and pooling</em></p>
<p>Small craft and SCUBA were used to sample&nbsp;Southern and Central California, USA subtidal coastal waters. Foot tissue from 46 <em>K. kelletii&nbsp;</em>(urn:lsid:marinespecies.org:taxname:491054)<em>&nbsp;</em>adults (&gt;60 mm shell length; Rosenthal 1970) – 23 individuals in 2015 and 23 individuals in 2016 – were sampled non-lethally from each of 13 subtidal locations (~15 m depth) across the species’ historical and expanded range. By only including adults, we aimed to represent the local, established population and avoid the bias in population structure that could arise from recent recruitment if juveniles were included. Collected tissue samples were then frozen on dry ice or liquid nitrogen for transport to the California Polytechnic State University (San Luis Obispo, CA) and stored at -80 ℃ until processed for DNA extraction.</p>
<p>DNA extraction was performed using an optimized version of the ‘salting-out’ protocol developed by Li et al. (2011) and modified by Daniels et al. (2023a), where the full extraction protocol is detailed. Briefly, 30 mg of tissue was lysed with proteinase K and RNase A in a warm water bath. Subsequently, DNA was separated from proteins, which precipitated in the presence of ammonium acetate by centrifugation, and was then purified from the supernatant via ethanol washes. Finally, precipitated DNA was resuspended in Tris-EDTA (1xTE) buffer and stored at -20 ºC until further analyses.</p>
<p>DNA quality was assessed visually using a 1% agarose gel in Tris-Acetic Acid-EDTA (TAE) buffer, GelRed (Biotium, Inc) gel stain, and referenced to the 200–10,000 bp Hyperladder I (Bioline, Meridian Bioscience). Because 91.3% of all extractions produced high molecular weight bands (&gt;10 kb) with faint smears from degraded DNA, all specimens were included in the study. Extractions were quantified using the AccuClear Ultra High Sensitivity dsDNA quantification kit (Biotium, Inc) with 3 standards and measured using a SpectraMax M2 microplate reader (Molecular Devices, LLC). Finally, an equimolar amount of DNA from each of the 46 individuals collected at each location was pooled by the collection site (population), ensuring that each library had the same number of individuals. In total, 598 individuals belonging to 13 populations spanning approximately 800 km were included in the analysis.</p>
<p><em>Library preparation and sequencing</em></p>
<p>Equimolar pooled ezRAD (Toonen et al. 2013) libraries were generated following the detailed protocol of Knapp et al. (2016) for all 13 sites. Briefly, genomic DNA was digested using the isoschizomer restriction enzymes <em>Mbo</em>I and <em>Sau</em>3AI (New England Biolabs, Ipswich, MA). Digestions were performed in a total volume of 50 µl, containing 25 µl of dsDNA (~1 µg), 5 µl of NEB Cutsmart Buffer (provided with restriction enzymes), 18 µl of HPLC grade water, 1 µl <em>Mbo</em>I (10 units), and 1 µl <em>Sau3</em>AI (10 units) under the following thermocycler profile: 37 ºC for 18 h, then deactivation at 65 ºC for 20 min. After digestion, samples were cleaned using Mag-Bind TotalPure NGS (Omega Bio-Tek) beads at a 1:1.18 (DNA:beads) ratio to remove fragments &lt; 200 bp (Norcross, GA). Libraries were prepared for sequencing using the KAPA Hyper Prep DNA kit (Roche Sequencing and Life Science) following a modified version of the manufacturer protocol (see Knapp et al. 2016). Quality control by a Bioanalyzer and sequencing of the libraries on one lane of an Illumina HiSeq2500 were performed in the DNA Technologies and Expression Analysis Core Laboratory at the University of California (Davis, CA).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924537 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924537
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924505 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924505
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924604 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924604
completed
Robert J. Toonen
University of Hawaiʻi at Mānoa
808-236-7401
Hawaii Institute of Marine Biology 46-007 Lilipuna Rd
Kaneohe
HI
96744
USA
rjtoonen@gmail.com
pointOfContact
Crow White
Cal Poly San Luis Obispo
805-756-2954
California Polytechnic State University 1 Grand Avenue
San Luis Obispo
CA
93407
US
cwhite31@calpoly.edu
pointOfContact
Mark Christie
Purdue University
christ99@purdue.edu
pointOfContact
Benjamin Daniels
Oregon State University
ben.daniels255@gmail.com
pointOfContact
Jean Davidson
Cal Poly San Luis Obispo
jdavid06@calpoly.edu
pointOfContact
Freel Evan
University of Hawaiʻi at Mānoa
ebfreel@hawaii.edu
pointOfContact
Andy Lee
Purdue University
lee3617@purdue.edu
pointOfContact
Cataixa López
University of Hawaiʻi at Mānoa
clopezba@ull.edu.es
pointOfContact
asNeeded
Dataset Version: 1
Unknown
CLNo
CapLabel
SiteDescription
SiteCode
Lat
Lon
SiteCodeLetter_cap
Whelk_ID
TissueType
Year
ExtractionCap
DateOfExtraction
PerformedBy
OriginalCalculatedConcentration
Elution_TEBuffer
DNAYield
Measurement
PoolRADseq
Illumina HiSeq2500
SpectraMax M2 microplate reader (Molecular Devices, LLC)
thermocycler
theme
None, User defined
sample identification
site
Site_ID
latitude
longitude
stage
year
date
person name
genetic material concentration
volume
length
flag
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
plate reader
Thermal Cycler
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: RUI: Combined spatial and temporal analyses of population connectivity during a northern range expansion
https://osprey.bco-dmo.org/project/851109
Collaborative Research: RUI: Combined spatial and temporal analyses of population connectivity during a northern range expansion
<p><em>NSF Award Abstract:</em><br />
Where do young marine fish and shellfish come from? This project aims to improve our understanding of how coastal marine populations are connected in space and time. Coastal populations are replenished through the arrival of minuscule larvae that have been dispersed for weeks to months in the open ocean after spawning at remote sites. The combination of the long dispersal period of marine fish and shellfish larvae and the varying ocean currents results in complex patterns of "connectivity" among populations near and far. Identifying these patterns of connectivity is fundamental to marine science and critical for effective fisheries management and conservation, yet it remains an unresolved component of marine ecology. The study species is currently expanding its biogeographic range up the U.S. west coast. By genetically analyzing individuals from across the species' range, including offspring spawned in the laboratory by experimentally-crossed individuals collected in the field from throughout the species historical and expanded range, certain genes can serve to differentiate populations along the coast. The team leverages the statistical power of these geographically-informative genes to assign thousands of young collected in the field to the source populations that spawned them (across the species' range and over multiple years). The team then quantifies patterns of connectivity over multiple years, and tests fundamental hypotheses on the spatial scale, temporal variability, biogeographic patterns, and biophysical drivers of population connectivity. The project trains approximately two dozen U.S. university students in molecular ecology and marine science, as well as creating intellectual linkages among Ph.D.-granting and non-Ph.D.-granting universities. The project also supports further development of a K-12 education program that uses SCUBA diving and videography to teach elementary school students Next Generation Science Standards and train them for careers in science, technology, engineering and mathematics.</p>
<p>Using a kelp forest gastropod and fisheries species (Kellet's whelk, Kelletia kelletii), this project combines genome-wide Restriction site Associated DNA (RAD) loci with transcriptomic loci identified from common-garden laboratory crosses of individuals from the species' historical and expanded range to identify geographically-informative loci that maximize power for individual assignment testing. Leveraging the combined power of these loci, genetic assignment of approximately three thousand recruit samples to 20 putative source populations allows the team to construct three independent years of connectivity matrices and test some of the most fundamental questions in marine ecology, including: 1) Are marine populations open or closed and at what scales? 2) To what degree is the evolutionary pattern of gene flow represented by single versus multiple generations of connectivity events? And, 3) How spatially heterogeneous and temporally variable is population connectivity? Can one year of connectivity data predict anything about the next? Additionally, by focusing on a range-expanding species with common life history traits, the team addresses a number of questions with broad applicability and significant ecological and societal implications: 4) How much is population connectivity influenced by post-recruitment demographic and evolutionary processes? 5) How well-connected are historic- and expanded-range populations? And, of particular relevance to climate change, 6) Are El Nino oceanographic conditions, which are predicted to increase in frequency and intensity this century, driving the poleward range expansion of this coastal marine species? By coupling common-garden experimental crosses to identify maximally-informative transcriptomic loci with genomic RAD analysis of field samples, this project aims to accurately and precisely quantify marine population connectivity in high gene flow species with large population sizes.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
KW connectivity
largerWorkCitation
project
eng; USA
biota
oceans
-121.9391
-114.36197
27.15362
36.618167
2015-01-01
2017-12-31
California, USA and Baja, Mexico coast
0
BCO-DMO catalogue of parameters from Restriction site-associated DNA sequence metadata of Kelletia kelletii collected in California, USA and Baja, Mexico in 2015 to 2017
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/958433.rdf
Name: CLNo
Units: unitless
Description: <p>DNA extraction cap label number</p>
http://lod.bco-dmo.org/id/dataset-parameter/958434.rdf
Name: CapLabel
Units: unitless
Description: <p>DNA extraction cap label</p>
http://lod.bco-dmo.org/id/dataset-parameter/958435.rdf
Name: SiteDescription
Units: unitless
Description: <p>Name of Kelletia kelletii tissue sample collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/958436.rdf
Name: SiteCode
Units: unitless
Description: <p>Code name of Kelletia kelletii tissue sample collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/958437.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude of Kelletia kelletii tissue sample collection site, North is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/958438.rdf
Name: Lon
Units: decimal degrees
Description: <p>Longitude of Kelletia kelletii tissue sample collection site, West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/958439.rdf
Name: SiteCodeLetter_cap
Units: unitless
Description: <p>DNA extraction cap label letter</p>
http://lod.bco-dmo.org/id/dataset-parameter/958440.rdf
Name: Whelk_ID
Units: unitless
Description: <p>Unique sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/958441.rdf
Name: TissueType
Units: unitless
Description: <p>Sample tissue type (adult or recruit)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958442.rdf
Name: Year
Units: unitless
Description: <p>Year of Kelletia kelletii tissue sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/958443.rdf
Name: ExtractionCap
Units: unitless
Description: <p>DNA extraction cap label number</p>
http://lod.bco-dmo.org/id/dataset-parameter/958444.rdf
Name: DateOfExtraction
Units: unitless
Description: <p>Date DNA extraction was performed</p>
http://lod.bco-dmo.org/id/dataset-parameter/958445.rdf
Name: PerformedBy
Units: unitless
Description: <p>Researcher number who performed DNA extraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/958446.rdf
Name: OriginalCalculatedConcentration
Units: ug/ul
Description: <p>DNA extraction concentration (ng/ul) if measured</p>
http://lod.bco-dmo.org/id/dataset-parameter/958447.rdf
Name: Elution_TEBuffer
Units: uL
Description: <p>TE elution buffer used in DNA extraction protocol</p>
http://lod.bco-dmo.org/id/dataset-parameter/958448.rdf
Name: DNAYield
Units: ug
Description: <p>DNA extraction yield (ug), if measured</p>
http://lod.bco-dmo.org/id/dataset-parameter/958449.rdf
Name: Measurement
Units: mm
Description: <p>Kelletia kelletii maximum shell length (mm), if measured (recruits only)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958450.rdf
Name: PoolRADseq
Units: unitless
Description: <p>Flag if sample used in Pooled RADseq (1=yes, 0=no)</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
307571
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/cbc02f90-daf4-4a9a-bbe5-5b56a682be9f/content
download
https://doi.org/10.26008/1912/bco-dmo.958359.1
download
onLine
dataset
<p><em>Sample collection, DNA extraction, and pooling</em></p>
<p>Small craft and SCUBA were used to sample&nbsp;Southern and Central California, USA subtidal coastal waters. Foot tissue from 46 <em>K. kelletii&nbsp;</em>(urn:lsid:marinespecies.org:taxname:491054)<em>&nbsp;</em>adults (&gt;60 mm shell length; Rosenthal 1970) – 23 individuals in 2015 and 23 individuals in 2016 – were sampled non-lethally from each of 13 subtidal locations (~15 m depth) across the species’ historical and expanded range. By only including adults, we aimed to represent the local, established population and avoid the bias in population structure that could arise from recent recruitment if juveniles were included. Collected tissue samples were then frozen on dry ice or liquid nitrogen for transport to the California Polytechnic State University (San Luis Obispo, CA) and stored at -80 ℃ until processed for DNA extraction.</p>
<p>DNA extraction was performed using an optimized version of the ‘salting-out’ protocol developed by Li et al. (2011) and modified by Daniels et al. (2023a), where the full extraction protocol is detailed. Briefly, 30 mg of tissue was lysed with proteinase K and RNase A in a warm water bath. Subsequently, DNA was separated from proteins, which precipitated in the presence of ammonium acetate by centrifugation, and was then purified from the supernatant via ethanol washes. Finally, precipitated DNA was resuspended in Tris-EDTA (1xTE) buffer and stored at -20 ºC until further analyses.</p>
<p>DNA quality was assessed visually using a 1% agarose gel in Tris-Acetic Acid-EDTA (TAE) buffer, GelRed (Biotium, Inc) gel stain, and referenced to the 200–10,000 bp Hyperladder I (Bioline, Meridian Bioscience). Because 91.3% of all extractions produced high molecular weight bands (&gt;10 kb) with faint smears from degraded DNA, all specimens were included in the study. Extractions were quantified using the AccuClear Ultra High Sensitivity dsDNA quantification kit (Biotium, Inc) with 3 standards and measured using a SpectraMax M2 microplate reader (Molecular Devices, LLC). Finally, an equimolar amount of DNA from each of the 46 individuals collected at each location was pooled by the collection site (population), ensuring that each library had the same number of individuals. In total, 598 individuals belonging to 13 populations spanning approximately 800 km were included in the analysis.</p>
<p><em>Library preparation and sequencing</em></p>
<p>Equimolar pooled ezRAD (Toonen et al. 2013) libraries were generated following the detailed protocol of Knapp et al. (2016) for all 13 sites. Briefly, genomic DNA was digested using the isoschizomer restriction enzymes <em>Mbo</em>I and <em>Sau</em>3AI (New England Biolabs, Ipswich, MA). Digestions were performed in a total volume of 50 µl, containing 25 µl of dsDNA (~1 µg), 5 µl of NEB Cutsmart Buffer (provided with restriction enzymes), 18 µl of HPLC grade water, 1 µl <em>Mbo</em>I (10 units), and 1 µl <em>Sau3</em>AI (10 units) under the following thermocycler profile: 37 ºC for 18 h, then deactivation at 65 ºC for 20 min. After digestion, samples were cleaned using Mag-Bind TotalPure NGS (Omega Bio-Tek) beads at a 1:1.18 (DNA:beads) ratio to remove fragments &lt; 200 bp (Norcross, GA). Libraries were prepared for sequencing using the KAPA Hyper Prep DNA kit (Roche Sequencing and Life Science) following a modified version of the manufacturer protocol (see Knapp et al. 2016). Quality control by a Bioanalyzer and sequencing of the libraries on one lane of an Illumina HiSeq2500 were performed in the DNA Technologies and Expression Analysis Core Laboratory at the University of California (Davis, CA).</p>
Specified by the Principal Investigator(s)
<p><em>Data filtering and SNPs calling</em></p>
<p>Libraries were initially trimmed to remove low-quality bases and adapters using dDocent v.2.9.4 (Puritz et al. 2014), obtaining an average of 16,640,463 reads per sample. The population of Monterey had the lowest number of reads, with 4,439,406, while Yellow Banks had the highest number, with 45,795,618 reads. The same pipeline was used to align the reads using BWA (mem algorithm) to the&nbsp;<em>K. kelletii&nbsp;</em>reference genome, which contains 2,107,417,620 base pairs (2.1 Gb) in 46,654 contigs and a complete BUSCO score of 84.1% (Daniels et al. 2023b).</p>
<p>SNPs were identified using FreeBayes (Garrison &amp; Marth 2012) implemented in dDocent, by calling variants from merged bam files produced by the pipeline. The TotalRawSNPs.vcf file contained 18,327,457 shared SNPs with a mean depth distribution of 5.04, which was filtered through VCFtools v 0.1.16 (Danecek et al. 2011) using the following parameters: maf 0.05, minQ30, and min-meanDP20. To address the potential effect of missing data in our results, we generated a series of files using the filter –max-missing as implemented in vcftools, from most restrictive option (no missing data, max-missing 1) to a very relaxed one (50% missing data, max-missing 0.50). Further filters were explored in AssessPool (github.com/ToBoDev/assessPool), a bioinformatic program designed to filter, analyze, and visualize pool-seq data (Freel 2024). Downstream analyses only included loci with max-missing 0.75 and 30x coverage, which kept reliable SNPs calling with RADseq data while avoiding overrepresented loci with higher quality scores (Bentley et al. 2008, Li 2014, Rivera-Colón &amp; Catchen 2021).</p>
<p><em>Population genetic analyses</em></p>
<p>The final vcf filtered file produced was imported to TASSEL v. 5 (Bradbury et al. 2007) to explore population similarities via Principal Component Analysis (PCA). Population genetic differentiation between sites was calculated based on pairwise estimates of&nbsp;<em>F</em><sub>ST</sub>&nbsp;using PoPoolation2, implemented in AssesPool, which also calculates pairwise significance (<em>p-</em>values) using Fisher’s Exact Test (Kofler et al. 2011). We also compared the matrix of our pairwise estimates of genetic differentiation to those obtained by White et al. (2010), where the authors analyzed between 50 and 92 individuals per population from the Southern California Bight using 9 microsatellite DNA loci. For the collection sites shared between both studies (ANN, COJ, ISV, JAL and YEL), we compared&nbsp;<em>F</em><sub>ST</sub>&nbsp;values using a Mantel test in the vegan R package with 9999 permutations to test for significantly correlated results (v. 2.5–7; Oksanen et al. 2020).&nbsp;</p>
Specified by the Principal Investigator(s)
- Import "KW_DNA_PooledezRAD.xlsx" into BCO-DMO system with formatting
- Convert DateOfExtraction to YYYY-MM-DD
- Adjust parameter names to remove units
- Converted Lon to negative for West is negative representation
- Export file as "958359_v1_kelletia_kelletii_pooled_rad.csv"
Accepted species identifier confirmed on 2025-04-09.
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina HiSeq2500
Illumina HiSeq2500
PI Supplied Instrument Name: Illumina HiSeq2500 PI Supplied Instrument Description:Quality control by a Bioanalyzer and sequencing of the libraries on one lane of an Illumina HiSeq2500 were performed in the DNA Technologies and Expression Analysis Core Laboratory at the University of California (Davis, CA). Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
SpectraMax M2 microplate reader (Molecular Devices, LLC)
SpectraMax M2 microplate reader (Molecular Devices, LLC)
PI Supplied Instrument Name: SpectraMax M2 microplate reader (Molecular Devices, LLC) PI Supplied Instrument Description:Extractions were quantified using the AccuClear Ultra High Sensitivity dsDNA quantification kit (Biotium, Inc) with 3 standards and measured using a SpectraMax M2 microplate reader (Molecular Devices, LLC). Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
thermocycler
thermocycler
PI Supplied Instrument Name: thermocycler PI Supplied Instrument Description:Briefly, genomic DNA was digested using the isoschizomer restriction enzymes MboI and Sau3AI (New England Biolabs, Ipswich, MA). Digestions were performed in a total volume of 50 µl, containing 25 µl of dsDNA (~1 µg), 5 µl of NEB Cutsmart Buffer (provided with restriction enzymes), 18 µl of HPLC grade water, 1 µl MboI (10 units), and 1 µl Sau3AI (10 units) under the following thermocycler profile: 37 ºC for 18 h, then deactivation at 65 ºC for 20 min. Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)