home > bioproject > PRJEB1830
identifier PRJEB1830
type bioproject
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organism
title ZF_MrSol
description The Zebrafish is becoming a popular model organism for developmental biology and human disease. This increasing popularity has resulted in a demand for reverse genetics, which has traditionally been neglected in favour of forward genetic approaches because of the lack of an efficient gene knockout (KO) technology. Thousands of phenotypes have been identified using forward genetic approaches, but time consuming positional cloning has slowed the identification of the genes involved. Morpholino oligonucleotides have become the method of choice for gene knockdown in the Zebrafish, but are restricted to early processes, and insertional mutagenesis has also become a popular method for gene led investigations. However, this still does not allow the targeted knockdown of genes of choice. More recently, zinc finger nucleases have been shown to be effective for gene targeting, but this method can be expensive and labour intensive, and is not seen as practical for the KO of hundreds of genes. A project to sequence and finish (to 99.9% accuracy) the Zebrafish genome (one of only 3 vertebrate genomes to be completed to this accuracy, alongside human and mouse) has contributed to the effectiveness of a process termed TILLING, first described in arabadopsis and worm, to be used to create Zebrafish targeted alleles. This method traditionally uses cel-1 nuclease and fragment analysis to identify mutations, which is labour intensive and misses mutations, especially near SNPs, which are common. Here we show that by using re-sequencing, we are able to identify more mutations. Using this method we have screened 2 ENU mutagenised living libraries in 2 years, and identified ~200 KO. In total, the ZF Models Workpackage 4 collaboration has identified 243 Mutations in the Zebrafish, which will be publicly available via Ensembl, The Sanger Institute and ZIRC. In addition to identifying deleterious mutations in the Zebrafish, the Sanger Institiute has committed to describing the phenotype of all mutations created during this project. Both morphological and molecular (by microarray or transcript counting on the Illumina platform) phenotypes will be described and published via ensembl and Zfin. The advent of next generation sequencing technologies has significantly changed the amount of mutations that can be identified. We are now investigating the use of sequence capture (rather than PCR) for exon enrichment from mutagenised individuals. This will mean a further increase in throughput, and has opened up the possibility of identifying a non-sense allele in every protein coding gene within a reasonable time frame and budget.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
data type Exome
organization
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{...}
dbXrefs
sra-run  ERR031103ERR031104ERR031105ERR031106ERR031107ERR031108ERR034128ERR034129ERR034130ERR034131 More
sra-submission  ERA023121ERA029960ERA030774ERA032066ERA033220ERA034039ERA039681ERA042714ERA046548ERA047544 More
biosample  SAMEA905909SAMEA905905SAMEA905906SAMEA905907SAMEA905908SAMEA905901SAMEA906038SAMEA906082SAMEA906037SAMEA906032 More
sra-study  ERP000426
sra-sample  ERS014623ERS014624ERS014625ERS014626ERS014627ERS014628ERS017662ERS017670ERS017663ERS017664 More
sra-experiment  ERX011390ERX011392ERX011393ERX011394ERX011391ERX011389ERX012667ERX012661ERX012664ERX012656 More
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status public
visibility unrestricted-access
dateCreated 2011-03-15T00:00:00+0000
dateModified 2011-03-15T00:00:00+0000
datePublished 2011-03-15T00:00:00+0000