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
CN187635CN187635EST
CN187636CN187636EST
CN187637CN187637EST
CN187638CN187638EST
CN187639CN187639EST
CN187640CN187640EST
CN187641CN187641EST
CN187642CN187642EST
CN187643CN187643EST
CN187644CN187644EST
CN187645CN187645EST
CN187646CN187646EST
CN187647CN187647EST
CN187648CN187648EST
CN187649CN187649EST
CN187650CN187650EST
CN187651CN187651EST
CN187652CN187652EST
CN187653CN187653EST
CN187654CN187654EST
CN187655CN187655EST
CN187656CN187656EST
CN187657CN187657EST
CN187658CN187658EST
CN187659CN187659EST

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