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
CN189728CN189728EST
CN189729CN189729EST
CN189730CN189730EST
CN189731CN189731EST
CN189732CN189732EST
CN189733CN189733EST
CN189734CN189734EST
CN189735CN189735EST
CN189738CN189738EST
CN189739CN189739EST
CN189740CN189740EST
CN189741CN189741EST
CN189743CN189743EST
CN189744CN189744EST
CN189745CN189745EST
CN189746CN189746EST
CN189747CN189747EST
CN189748CN189748EST
CN189749CN189749EST
CN189750CN189750EST
CN189751CN189751EST
CN189752CN189752EST
CN189753CN189753EST
CN189754CN189754EST
CN189755CN189755EST

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