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
CX047048CX047048EST
CX047049CX047049EST
CX047050CX047050EST
CX047051CX047051EST
CX047052CX047052EST
CX047053CX047053EST
CX047054CX047054EST
CX047057CX047057EST
CX047058CX047058EST
CX047059CX047059EST
CX047060CX047060EST
CX047061CX047061EST
CX047062CX047062EST
CX047063CX047063EST
CX047064CX047064EST
CX047065CX047065EST
CX047066CX047066EST
CX047067CX047067EST
CX047068CX047068EST
CX047069CX047069EST
CX047070CX047070EST
CX047071CX047071EST
CX047072CX047072EST
CX047073CX047073EST
CX047074CX047074EST

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