Standard Operating Procedures (SOP’s)

A comprehensive list of Standard Operating Procedures (i.e. protocols) for various lab procedures can be found below. The SOP’s are organized by lab or area of focus.

General Lab SOP’s

GE-001.00 Procedure to Make 25X TBE

GE-002.00 Procedure to Make ProteinaseK (PK) Buffer

GE-003.00 Procedure to Make TEQ Buffer

GE-004.00 Procedure to Prepare SDS solution (10%,20%)

GE-005.00 Procedure to Prepare Lysis Buffer Ia for Lysis Buffer Blood Extraction

GE-006.00 Procedure to Prepare Lysis Buffer II for Lysis Buffer Blood Extraction

GE-007.00 Procedure to make 1x Tris-EDTA (TE) Buffer

GE-008.00 Procedure to make 5M NaCl solution

GE-009.00 Procedure to make Lysis Buffer for Hoess and Paabo DNEasy Extraction Protocol

GE-010.00 Procedure to make L2 Buffer

GE-011.00 Procedure to make LiCl Extraction Buffer

GE-012.00 Procedure to prepare STE Buffer

GE-013.00 Procedure to make a 5M LiCl solution

GE-014.00 Procedure to prepare Chloroform-Isoamyl

GE-015.00 Procedure to make 3M NaOac pH5.2

GE-016.00 Procedure to prepare Magic Buffer

GE-017.01 Procedure to make 20% Dimethylsulfoxide (DMSO) Salt saturated solution

GE-018.00 Procedure to make 5X orange G

GE-019.00 Procedure to prepare a 0.5M EDTA pH8.0 solution

GE-020.00 Procedure to make 1M Tris

GE-021.00 Procedure to make 1X PBS Buffer

GE-022.00 Procedure to make saturated NaCl solution

GE-023.00 Procedure to operate the pH meter

GE-024.00 Procedure to autoclave liquids and solids

GE-025.00 How to keep a lab notebook

GE-026.00 Lab Rules and Etiquette

GE-027.00 Procedure to print extraction dot labels

GE-028.00 Procedure to print dot labels for aliquots

GE-029.00 Procedure to print chemical labels for reagent bottles

GE-032.00 Procedure to make 1% DTT solution

GE-033.00 Procedure to make Lifton’s Buffer

GE-034 .00 Procedure to make Hybridization Buffer

GE-035.00 Procedure to Make 1x Low Tris-EDTA (TE) Buffer pH 7.5 (from solution)

Pre-PCR Lab SOP’s

PR-003.00 Extraction of DNA from Tissue Using Sodium Chloride (NaCl)

PR-005.00 Extraction of DNA from nucleated blood using lysis buffers

PR-006.00 Extraction of DNA from tissue using DNEasy kit

PR-010.01 Preparation of Extraction Grid

PR-011.00 Extraction Evaluation

PR-012.00 Quantification of DNA using Nanodrop® ND-1000 Spectrophotometer

PR-014.00 Procedure to prepare and aliquot Proteinase K

PR-015.00 Procedure to aliquot Taq polymerase

PR-016.00 Procedure to prepare and aliquot deoxynucleotide triphosphates (dNTPs) mix (100mM)

PR-017.00 Procedure to prepare a Polymerase Chain Reaction (PCR)

PR-019.00 Quantifying DNA using the Perkin Elmer® VictorX3(tm) 2030 Multilabel Reader

PR-022.00 Procedure to Determine Gender of Cetaceans using real time Polymerase Chain Reaction (q-PCR)

PR-026.00 Procedure to Quantify Nuclear DNA using BMI1 Primers and the Strategene MXP qPCR Machines

PR-027.01 Procedure to Quantify Mitochondrial DNA using CET12s Primers and the Strategene MXP qPCR Machines

PR-028.00 Procedure to Determine Gender of Pinnipeds and Cetaceans Using Polymerase Chain Reaction (PCR)_SR

PR-029.00 Procedure to prepare a multiplex(PCR)

PR-030.00 Quantifying DNA using Quant-iT ™ dsDNA Assay Kits and the Perkin Elmer® VictorX3(tm) 2030 Multilabel Reader

PR-031.00 Procedure To Transfer DNA From 1.7ml tubes to 1.1ml micronic tubes

PR-033.00 Procedure to Determine Gender of Pinnipeds using real time Polymerase Chain Reaction (q-PCR)

PR-034.00_Procedure to extract DNA using NucleoMag Manual Bead Protocol

PR-035.00 Procedure to extract DNA from tissue using the Machery-Nagel NucleoMag® Tissue kit

PR-036.00 Procedure to Resuspend and Dilute Primers

PR-038.00 Procedure to Quantify using the Qubit

PR-039.00 Procedure to Extract DNA from Fecal Material using QIAamp Fast DNA Mini Stool Kit

PR-040.01 Procedure to prepare ROX for qPCR runs

Post-PCR Lab SOP’s

PO-001.00 Procedure to Prepare Agarose Gel for Electrophoresis

PO-002.00 Performing Agarose Gel Electrophoresis

PO-003.00 Procedure to Prepare1X TBE

PO-004.00 Procedure to set up microsatellite plate on the ABI 3730

PO-006.00 Procedure for purifying PCR product with the QIAquick PCR purification kit

PO-005.00 Procedure to prepare an Amplifluor SNPs Genotyping reaction

PO-007.00 Procedure for Purifying PCR Product with Exo-SAP

PO-008.00 Procedure for preparing a Cycle Sequence reaction

PO-009.00 Purification of DNA Sequencing Reactions Using BigDye XTerminator

PO-010.00 Procedure to prepare and aliquot ExoSAP

PO-011.00 Procedure to prepare and aliquot BigDye v3.1 with 5X BigDye Buffer

PO-012.00 Procedure to Aliquot HiDi formamide

PO-013.00 Procedure to use the Zymoclean Gel DNA Recovery Kit

PO-014.00 Procedure for Agarose-based Sex Determination

PO-017.00 Operation and Maintenance of the ABI 3730 Genetic Analyzer

PO-019.00 Procedure to make serial dilutions from pre-made Standard Clones for CET12s and BMI assays

PO-020.00 Procedure to purify DNA Sequencing reactions using CleanSEQ

PO-021.01 Procedure to Quantify using the Qubit and Qubit Flex

Next Generation Sequencing (NGS) SOP’s

NG-001.02 Procedure to prepare Indexed libraries for sequencing on Illumina Genome Analyzers using Agilent capture array hybridization or Shotgun methods

NG-002.01 Procedure to archive Next Generation Sequencing (NGS) fastq data files_

NG-005.00 Procedure to clean the MiSeq

NG-007.00 Procedure to Prepare GtSEQ NGS Library

NG-008.00 Procedure for Epigenetics for Aging using Targeted Amplicons

NG-010.00 Procedure to Quanitfy Illumina adapted PCR product using Kapa standards