Washington Navel Orange Stored Fruit Pulp cDNA Library

Overview
Library NameWashington Navel Orange Stored Fruit Pulp cDNA Library
Unique NameWashington Navel Orange Stored Fruit Pulp 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. Pulp 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 Pulp 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
CN185700CN185700EST
CN185701CN185701EST
CN185702CN185702EST
CN185703CN185703EST
CN185704CN185704EST
CN185705CN185705EST
CN185706CN185706EST
CN185707CN185707EST
CN185708CN185708EST
CN185709CN185709EST
CN185710CN185710EST
CN185711CN185711EST
CN185712CN185712EST
CN185713CN185713EST
CN185714CN185714EST
CN185715CN185715EST
CN185716CN185716EST
CN185717CN185717EST
CN185720CN185720EST
CN185721CN185721EST
CN185722CN185722EST
CN185723CN185723EST
CN185724CN185724EST
CN185725CN185725EST
CN185726CN185726EST

Pages

Properties
Property NameValue
Genbank library cultivarWashington navel
Genbank library dev stageCommercially producing trees
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. Pulp 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 typePulp
Endocarptissue type