Parent Washington Navel Orange Callus cDNA Library UCRCS08-2

Overview
Library NameParent Washington Navel Orange Callus cDNA Library UCRCS08-2
Unique NameParent Washington Navel Orange Callus cDNA Library UCRCS08-2
OrganismCitrus sinensis (Sweet orange)
Typecdna_library
Vector: Lambda Uni-ZAP XR, excised phagemid; Site_1: EcoRI; Site_2: XhoI; Parent Washington navel orange embryogenic callus was established from undeveloped ovules of ca. 10 mm diameter young fruits under open pollination on Murashige-Skoog medium at 25oC with 16 h light in a tissue culture room. Embryogenic callus, globular and heart stage embryoids were pooled in approximately equal portions in RNAlater (Ambion), then RNA was extracted using TRIZOL Reagent (Invitrogen). Poly(A) RNA was purified from 500 microgram of total RNA using Qiagen Oligotex. A primary cDNA library was produced using a lambda ZAP XR cDNA Synthesis Kit (Stratagene). These steps were performed by Xinrong Ye (Roose lab, UC Riverside). One million pfu from the primary library were mass excised to produce a phagemid population by Raymond Fenton (Close lab, UC Riverside). 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 to UC Riverside (by Close), then processed at UC Riverside (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 NameParent Washington Navel Orange Callus cDNA Library UCRCS08-2
OrganismCitrus sinensis (Sweet orange)
Typecdna_library
Features
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Feature NameUnique NameType
CX069543CX069543EST
CX069544CX069544EST
CX069545CX069545EST
CX069546CX069546EST
CX069547CX069547EST
CX069548CX069548EST
CX069549CX069549EST
CX069550CX069550EST
CX069551CX069551EST
CX069552CX069552EST
CX069553CX069553EST
CX069554CX069554EST
CX069555CX069555EST
CX069556CX069556EST
CX069557CX069557EST
CX069558CX069558EST
CX069559CX069559EST
CX069560CX069560EST
CX069561CX069561EST
CX069562CX069562EST
CX069565CX069565EST
CX069566CX069566EST
CX069567CX069567EST
CX069568CX069568EST
CX069569CX069569EST

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Properties
Property NameValue
Callustissue type
Genbank library cultivarWashington navel
Genbank library dev stageEmbryogenic and embryoid
Genbank library noteVector: Lambda Uni-ZAP XR, excised phagemid; Site_1: EcoRI; Site_2: XhoI; Parent Washington navel orange embryogenic callus was established from undeveloped ovules of ca. 10 mm diameter young fruits under open pollination on Murashige-Skoog medium at 25oC with 16 h light in a tissue culture room. Embryogenic callus, globular and heart stage embryoids were pooled in approximately equal portions in RNAlater (Ambion), then RNA was extracted using TRIZOL Reagent (Invitrogen). Poly(A) RNA was purified from 500 microgram of total RNA using Qiagen Oligotex. A primary cDNA library was produced using a lambda ZAP XR cDNA Synthesis Kit (Stratagene). These steps were performed by Xinrong Ye (Roose lab, UC Riverside). One million pfu from the primary library were mass excised to produce a phagemid population by Raymond Fenton (Close lab, UC Riverside). 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 to UC Riverside (by Close), then processed at UC Riverside (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 typeCallus