Washington Navel Orange Stored Fruit Rind cDNA Library

Overview
Library NameWashington Navel Orange Stored Fruit Rind cDNA Library
Unique NameWashington Navel Orange Stored Fruit Rind cDNA Library
OrganismCitrus sinensis (Sweet orange)
Typecdna_library
Vector: Lambda Uni-ZAP XR, excised phagemid; Site_1: EcoRI; Site_2: XhoI; Fruits were collected January-March 2003 (Federici, Roose lab; Focht, Sievert & Robinson, Arpaia lab). Four samples related to storage conditions were produced: 1) fresh-picked in Mentone (Arnott Brothers Enterprises, Mentone, CA), 2) after 21 days storage at 5C at Kearney then transported to UC Riverside on ice, 3) after 5 additional days storage at 11C at Kearney, sampled immediately, 4) fruit grown in southern CA were obtained from Redlands Foothill Packing House after commercial packing, X-ray irradiated at 300 Gy by Surebeam, then stored 1 day at ambient temperature. Rind tissue (juice vesicles) were collected. Tissues were snap frozen and then stored at -80C until further processing. Fenton (Close lab) purified RNA by the phenol method described in J. Japanese Soc. Hort. Sci. 1996. 64 (4): 809-814, purified poly(A) mRNA using a PolyATtrack mRNA Isolation System IV (Promega), produced a primary cDNA library using a lambda ZAP XR cDNA Synthesis Kit (Stratagene), then mass-excised one million pfu from the primary library to produce a phagemid population. Phagemids were plated, plasmid DNA purified, cDNA clones archived, and DNA sequences determined bi-directionally using an ABI3730 at the Arizona Genomics Institute, University of Arizona (Kim, Kudrna, Stum, Yost, Wing). Chromatogram files were downloaded by FTP to UC Riverside (by Close), then processed at UC Riverside (by Wanamaker, Close lab) using the HarvEST pipeline (http://harvest.ucr.edu) to remove vector and cloning oligo sequences and various contaminants, and to trim to a high quality region. Sequences that retained a phred 17 region of at least 100 bases were deposited to GenBank.
SNP Chip Base
Array NameWashington Navel Orange Stored Fruit Rind cDNA Library
OrganismCitrus sinensis (Sweet orange)
Typecdna_library
Features
The following browser provides a quick view for new visitors. Use the searching mechanism to find specific features.
Feature NameUnique NameType
CN189197CN189197EST
CN189198CN189198EST
CN189199CN189199EST
CN189201CN189201EST
CN189202CN189202EST
CN189203CN189203EST
CN189204CN189204EST
CN189205CN189205EST
CN189206CN189206EST
CN189207CN189207EST
CN189208CN189208EST
CN189209CN189209EST
CN189210CN189210EST
CN189211CN189211EST
CN189212CN189212EST
CN189213CN189213EST
CN189214CN189214EST
CN189215CN189215EST
CN189216CN189216EST
CN189217CN189217EST
CN189218CN189218EST
CN189219CN189219EST
CN189220CN189220EST
CN189221CN189221EST
CN189222CN189222EST

Pages

Properties
Property NameValue
Genbank library cultivarWashington navel
Genbank library dev stageCommercially producing trees
Pericarptissue type
Genbank library noteVector: Lambda Uni-ZAP XR, excised phagemid; Site_1: EcoRI; Site_2: XhoI; Fruits were collected January-March 2003 (Federici, Roose lab; Focht, Sievert & Robinson, Arpaia lab). Four samples related to storage conditions were produced: 1) fresh-picked in Mentone (Arnott Brothers Enterprises, Mentone, CA), 2) after 21 days storage at 5C at Kearney then transported to UC Riverside on ice, 3) after 5 additional days storage at 11C at Kearney, sampled immediately, 4) fruit grown in southern CA were obtained from Redlands Foothill Packing House after commercial packing, X-ray irradiated at 300 Gy by Surebeam, then stored 1 day at ambient temperature. Rind tissue (juice vesicles) were collected. Tissues were snap frozen and then stored at -80C until further processing. Fenton (Close lab) purified RNA by the phenol method described in J. Japanese Soc. Hort. Sci. 1996. 64 (4): 809-814, purified poly(A) mRNA using a PolyATtrack mRNA Isolation System IV (Promega), produced a primary cDNA library using a lambda ZAP XR cDNA Synthesis Kit (Stratagene), then mass-excised one million pfu from the primary library to produce a phagemid population. Phagemids were plated, plasmid DNA purified, cDNA clones archived, and DNA sequences determined bi-directionally using an ABI3730 at the Arizona Genomics Institute, University of Arizona (Kim, Kudrna, Stum, Yost, Wing). Chromatogram files were downloaded by FTP to UC Riverside (by Close), then processed at UC Riverside (by Wanamaker, Close lab) using the HarvEST pipeline (http://harvest.ucr.edu) to remove vector and cloning oligo sequences and various contaminants, and to trim to a high quality region. Sequences that retained a phred 17 region of at least 100 bases were deposited to GenBank.
Genbank library tissue typeRind