Ruby Orange Developing Seed cDNA Library UCRCS09

Overview
Library NameRuby Orange Developing Seed cDNA Library UCRCS09
Unique NameRuby Orange Developing Seed cDNA Library UCRCS09
OrganismCitrus sinensis (Sweet orange)
Typecdna_library
Vector: Lambda Uni-ZAP XR, excised phagemid; Site_1: EcoRI; Site_2: XhoI; Two trees with open-pollinated flowers in a mixed planting in the UC Riverside Citrus Variety Collection were the source of tissue. Developing seeds were collected by Federici (Roose lab) from May-July 2003. This included nine stages, based on size of fruit: 10-20 mm, 20-30 mm, 30-35 mm, 35-40 mm, 40-45 mm, 45-50 mm, 50-55 mm, 55-60 mm, 60-65 mm. Tissues were stored in RNA Later (Ambion) 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 an Oligotex mRNA Kit (Qiagen), produced a primary cDNA library using a lambda ZAP XR cDNA Synthesis Kit (Stratagene), then mass-excised 0.48 million pfu from the primary library to produce a phagemid population. The library was made from equal portions of RNA from seed at each of the nine fruit stages, but seeds were not of uniform size at any stage. Phagemids were plated, plasmid DNA purified, cDNA clones archived, and DNA sequences determined bi-directionally using an ABI3730 at DNA Landmarks (Landry, Hubert, Laforest, Landry, Ligonde). Chromatogram files were downloaded by FTP by Close, then processed 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 assembled, then chimeras were removed following manual inspection of assemblies (Close, Roose, Federici, Wanamaker, Lyon, Ye, Jang, Collin, Kacar, Ikeda, Quinitio). Sequences that survived all removal steps were submitted to GenBank.
SNP Chip Base
Array NameRuby Orange Developing Seed cDNA Library UCRCS09
OrganismCitrus sinensis (Sweet orange)
Typecdna_library
Features
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Feature NameUnique NameType
CX049230CX049230EST
CX049231CX049231EST
CX049232CX049232EST
CX049233CX049233EST
CX049234CX049234EST
CX049235CX049235EST
CX049236CX049236EST
CX049237CX049237EST
CX049240CX049240EST
CX049241CX049241EST
CX049242CX049242EST
CX049243CX049243EST
CX049244CX049244EST
CX049245CX049245EST
CX049246CX049246EST
CX049247CX049247EST
CX049248CX049248EST
CX049249CX049249EST
CX049252CX049252EST
CX049253CX049253EST
CX049254CX049254EST
CX049255CX049255EST
CX049256CX049256EST
CX049257CX049257EST
CX049258CX049258EST

Pages

Properties
Property NameValue
Genbank library cultivarRuby
Genbank library dev stage20 year old trees
Genbank library noteVector: Lambda Uni-ZAP XR, excised phagemid; Site_1: EcoRI; Site_2: XhoI; Two trees with open-pollinated flowers in a mixed planting in the UC Riverside Citrus Variety Collection were the source of tissue. Developing seeds were collected by Federici (Roose lab) from May-July 2003. This included nine stages, based on size of fruit: 10-20 mm, 20-30 mm, 30-35 mm, 35-40 mm, 40-45 mm, 45-50 mm, 50-55 mm, 55-60 mm, 60-65 mm. Tissues were stored in RNA Later (Ambion) 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 an Oligotex mRNA Kit (Qiagen), produced a primary cDNA library using a lambda ZAP XR cDNA Synthesis Kit (Stratagene), then mass-excised 0.48 million pfu from the primary library to produce a phagemid population. The library was made from equal portions of RNA from seed at each of the nine fruit stages, but seeds were not of uniform size at any stage. Phagemids were plated, plasmid DNA purified, cDNA clones archived, and DNA sequences determined bi-directionally using an ABI3730 at DNA Landmarks (Landry, Hubert, Laforest, Landry, Ligonde). Chromatogram files were downloaded by FTP by Close, then processed 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 assembled, then chimeras were removed following manual inspection of assemblies (Close, Roose, Federici, Wanamaker, Lyon, Ye, Jang, Collin, Kacar, Ikeda, Quinitio). Sequences that survived all removal steps were submitted to GenBank.
Genbank library tissue typeSeed
Seedtissue type