Lab Protocols

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Disclaimer
These protocols are presented so that others may adapt and possibly improve upon them. Every effort was made to make them accurate, but in some cases they were a work in progress and should not be relied on without independent validation.

Sensitive Issues

We recognize and acknowledge that certain audiences may be offended by research on animals and note that throughout the research we have taken all possible measures to preserve the welfare of the birds and cause no undue harm or interference. We conduct our research under the oversight of a federally mandated animal care committee, and we hope that our findings will ultimately be helpful to the animals themselves by learning more about their natural history and how best to contribute to their conservation.

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CC BY-NC-SA: http://creativecommons.org/licenses/by-nc-sa/3.0/

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Recent Submissions

Now showing 1 - 20 of 36
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    Protocol for steroid radioimmunoassay of plasma
    (2013-03-29) Joe Casto, Jodie Jawor, Danielle Whittaker
    This protocol can be used to measure the concentration of steroid hormones in small plasma samples. This protocol has been copied and modified from protocols provided by Dr. John Wingfield at the University of Washington. It has been written for use in the laboratory of Dr. Ellen Ketterson at Indiana University, and therefore the details may require modification if the procedure is performed elsewhere. The general procedure, which takes 4-5 days to complete, is described below. Prepared January 1998 by Joe Casto, modified December 2005 by Jodie Jawor and May 2010 by Danielle Whittaker.
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    Steroid Label Clean Up Protocol
    (2013-03-29) Unsure original creator, possibly updated by Kristal Cain?
    Protocol for cleaning radio-labeled steroid hormone
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    Recipe for Longmire's solution
    (2013-03-29) Ketterson/Nolan research group, Sara Schrock
    Recipe for making Longmire's solution, a cell lysis buffer for storing blood samples for DNA analysis. Also includes recipes for stock solutions used in making Longmire's solution.
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    Salt extraction of DNA from whole blood
    (2013-03-29) From Peter Dunn's lab; unsure if updated by Kettlab members
    Protocol for extracting DNA from whole blood stored in lysis buffer. Uses the salt solution extraction buffer.
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    Junco Female Ethogram
    (2013-03-29) Ian Parker-Renga
    An ethogram describing various categories of observed behavior, specific for female juncos.
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    Protocol for steroid radioimmunoassay of egg yolks
    (2013-03-29) Joe Lipar
    This protocol can be used to measure the concentration of steroid hormones in yolk samples. This protocol has been copied and modified from protocols provided by Dr. John Wingfield at the University of Washington and Dr. Hubert Schwabl at Washington State University. It has been written for use in the laboratory of Dr. Ellen Ketterson at Indiana University, and therefore the details may require modification if the procedure is performed elsewhere. The general procedure, which takes 5 days to complete, is described below. Variations and additional information are provided in the appendices. Prepared October 1997 by Joe Lipar.
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    Spectrometer Protocol
    (2013-03-29) Lynn Siefferman
    Protocol for using the spectrometer to analyze color spectrum from feather samples.
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    Excel worksheet for RIA
    (2013-03-29) Steve Schoech
    A spreadsheet for calculating steroid hormone concentrations from radioimmunoassay results. Calculates concentrations of progesterone, testosterone, estradiol, corticosterone, and dihydrotestosterone.
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    RNA extraction protocols
    (2013-03-29) Christine Bergeon Burns, Kimberly Rosvall
    Protocol for extraction of RNA from avian tissue using Trisol and includes instructions for gel electrophoresis.
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    Sperm Collecting and Counting Protocol
    (2013-03-29) George Gee, Elaina Tuttle, Tracey Kast
    Protocol for collecting sperm from songbirds, as well as for counting sperm samples. Also includes data sheet.
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    Preen Oil Collection Questions
    (2013-03-29) Danielle Whittaker
    Questions about methodology for collecting preen oil samples from dark-eyed juncos.
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    Short protocol for direct radioimmunoassay of corticosterone (a.k.a. Little B)
    (2013-03-29) Joe Casto, Jodie Jawor
    This protocol can be used to measure the concentration of corticosterone in small plasma samples. This protocol has been copied and modified from protocols provided by Dr. John Wingfield at the University of Washington. It has been written for use in the laboratory of Dr. Ellen Ketterson at Indiana University, and therefore the details may require modification if the procedure is performed elsewhere. The general procedure, which takes 4 days to complete, is described below. Variations and additional information are provided in the appendices. Prepared October 1999 by Joe Casto, modified October 2003 by Jodie Jawor.
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    Egg Yolk preparation
    (2013-03-29) Unsure original creator, possibly updated by Kristal Cain?
    Protocol to prepare frozen egg yolks for use in a variety of laboratory tests (ELIZA, Hormone assay, Carotenoid HPLC)
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    Protocol for phenol-chloroform extraction of DNA from whole blood samples
    (2013-03-29) Danielle Whittaker
    Protocol for extracting DNA from whole blood stored in lysis buffer. Uses the phenol-chloroform method of extraction.
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    Protocol for phenol-chloroform extraction of DNA from whole blood samples, with checklist
    (2013-03-29) Nicole Gerlach
    Protocol for extracting DNA from whole blood stored in lysis buffer. Uses the phenol-chloroform method of extraction. Modified from full protocol to include checklist for each step.
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    qPCR protocol
    (2013-03-29) Christine Bergeon Burns, Kimberly Rosvall
    Protocol for quantitative PCR to analyse RNA concentration from cDNA.
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    Protocol for kit extraction of DNA from whole blood samples
    (2013-03-29) Nicole Gerlach
    Protocol for extracting DNA from whole blood stored in lysis buffer. Uses IBI Scientific MINI Genomic DNA extraction kits. Includes checklist for each step.
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    Microsatellite PCR and ABI3730 Genotyping Instructions
    (2013-03-29) Danielle Whittaker, Nicole Gerlach
    Protocol for PCR of extracted avian DNA. Includes directions for PCR to amplify microsatellite loci (used for paternity analysis) and for PCR to amplify sex-specific loci (used for determining sample sex). Includes directions for PCR reactions as well as analysis of PCR product on the ABI3730. Also includes information on the primers used by the Ketterson lab for analyzing junco microsatellite loci.
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    Blood Sample Collection for DNA
    (2013-03-29) Ketterson/Nolan research group
    Protocol for collecting blood samples for later DNA extraction
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    Molecular sexing of birds
    (2013-03-29) Danielle Whittaker
    Protocol for PCR of extracted avian DNA using primers that can determine the sex of the samples. Uses agarose gels to determine the amplified alleles.