DNA Libraries - Mississippi Genome Exploration Laboratory - MGEL - Daniel G. Peterson - Genomics, Bioinformatics, Cytogenetics, Molecular Biology - Loblolly Pine, Pinus taeda, Gymnosperms, Cotton, Plant & Animal Pathogens/Pests, Cattle
Dixie Pix in action
MGEL's "Dixie Pix" robot hard at work

DNA LIBRARIES

Overview | Libraries | Library Naming Conventions

Overview

We are currently involved in the production of bacterial artificial chromosome (BAC) libraries and Cot-filtered libraries (see Cot Filtration & CBCS) from a variety of species.  The BAC and Cot-filtered libraries are being used in physical mapping, gene isolation, genome sequencing, and various forms of genome analysis conducted in our lab and the labs of our collaborators.  Below is a list of libraries that we have constructed, have helped to construct, or are in the process of constructing.  All libraries constructed as part of federal grants are available to any interested parties on a cost-recovery basis.  In some instances, MGEL does not distribute the DNA resources (e.g., libraries, clones, macroarrays, etc.) it generates  but rather has such services performed by organizations that specialize in molecular resource management and distribution (e.g., the Clemson University Genomics Institute and the Plant Genome Mapping Laboratory).  To learn more about a particular library (including vector, host, insert size, clone number, etc.) and information on its distributor, click on a link under the heading "Library Name."  See the Library Naming Conventions section below to learn how library names are developed.  Contact Daniel Peterson for additional details.

Libraries

Library Name Library Type
(see below)
Species & 'Cultivar, Strain, or Individual' Common name
PT_7Ba B Pinus taeda '7-56' Loblolly pine
TDD_Ba B Taxodium distichum Bald cypress
  CP_EBa B Crocodylus porosus 'Errol' Saltwater crocodile  
  RR_UBa B Rotylenchulus reniformis Reniform nematode  
  ZM_MP313EBa * B Zea mays 'MP313E' Maize  
GR__Ba B Gossypium raimondii D-genome cotton
GH_MBb B Gossypium hirsutum 'Maxxa' Upland cotton
VV_SBa B Vitis vinifera 'Syrah' Grape
SB_BSa S Sorghum bicolor 'BTx623' Grain sorghum
SB_BMa M Sorghum bicolor 'BTx623' Grain sorghum
SB_BMb M Sorghum bicolor 'BTx623' Grain sorghum
SB_BHa H Sorghum bicolor 'BTx623' Grain sorghum
TA_CTa T Triticum aestivum 'Chinese Spring' Bread wheat

*Library assigned name prior to adoption of standardized naming conventions


Library Naming Conventions

DNA libraries produced at MGEL are named using the conventions utilized by the Clemson University Genomics Institute and the Arizona Genomics Institute.  Each library name consists of six identification fields.  Below is an example of a file name broken into its six fields and a legend explaining the meaning and limits of each field.

Library naming

Field 1 - First letter of the genus of the organism from which the library was derived.  In the example, the T stands for Taxodium.

Field 2 - First letter of the species name of the organism from which the library was derived.  In the example, the D stands for distichum.

Field 3 - First letter of the subspecies from which the library was derived.  If a subspecies name is not known or not applicable, an underscore, _,  is used to show that the subspecies field is empty.  In the example above, the D stands for subspecies distichum.

Field 4 - First letter or number of the cultivar/genotype from which the library was derived.  As with the Field 3, an underscore can be used to indicate the lack of a known cultivar or genotype (as shown above).

Field 5 - A one letter abbreviation for the means by which the library was constructed.  At MGEL, we currently have libraries with the following Field 5 designations:

Field 6 - A one lowercase letter "wildcard" that can be used to differentiate similar libraries constructed from the same organism, e.g., a Taxodium distichum BAC library produced using a partial HindIII digestion might be assigned the wildcard "a" while a Taxodium distichum BAC library produced using a partial BstyI digestion might be assigned the wildcard "b."

Other Areas of Expertise: Bioinformatics | Cot Analysis | Cot Filtration & CBCS | Cytogenetics