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.
Features
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Feature NameUnique NameType
CX054054CX054054EST
CX054053CX054053EST
CX054052CX054052EST
CX054051CX054051EST
CX054050CX054050EST
CX054049CX054049EST
CX054048CX054048EST
CX054047CX054047EST
CX054046CX054046EST
CX054045CX054045EST
CX054044CX054044EST
CX054043CX054043EST
CX054042CX054042EST
CX054041CX054041EST
CX054040CX054040EST
CX054039CX054039EST
CX054038CX054038EST
CX054037CX054037EST
CX054036CX054036EST
CX054035CX054035EST
CX054034CX054034EST
CX054033CX054033EST
CX054032CX054032EST
CX054029CX054029EST
CX054028CX054028EST

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