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
CX047020CX047020EST
CX047021CX047021EST
CX047024CX047024EST
CX047025CX047025EST
CX047026CX047026EST
CX047027CX047027EST
CX047028CX047028EST
CX047029CX047029EST
CX047030CX047030EST
CX047031CX047031EST
CX047032CX047032EST
CX047033CX047033EST
CX047034CX047034EST
CX047035CX047035EST
CX047036CX047036EST
CX047037CX047037EST
CX047038CX047038EST
CX047039CX047039EST
CX047040CX047040EST
CX047041CX047041EST
CX047042CX047042EST
CX047043CX047043EST
CX047044CX047044EST
CX047045CX047045EST
CX047047CX047047EST

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