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
The following browser provides a quick view for new visitors. Use the searching mechanism to find specific features.
Feature NameUnique NameType
CX047177CX047177EST
CX047178CX047178EST
CX047179CX047179EST
CX047180CX047180EST
CX047181CX047181EST
CX047182CX047182EST
CX047183CX047183EST
CX047184CX047184EST
CX047185CX047185EST
CX047186CX047186EST
CX047187CX047187EST
CX047188CX047188EST
CX047189CX047189EST
CX047190CX047190EST
CX047192CX047192EST
CX047193CX047193EST
CX047194CX047194EST
CX047195CX047195EST
CX047196CX047196EST
CX047197CX047197EST
CX047198CX047198EST
CX047199CX047199EST
CX047200CX047200EST
CX047201CX047201EST
CX047202CX047202EST

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