Dataset Dfs_DrosDel_set1

General Information
Name	Dfs_DrosDel_set1	Species	D. melanogaster
Dataset type	aberration stock collection	FlyBase ID	FBlc0000498
Source & Content
Consists of	Fly stocks that comprise a set of molecularly defined deficiencies. (Ryder et al., 2007)
Created by
Available from	Bloomington Drosophila Stock Center Drosophila Genetic Resource Center, Kyoto, Japan
Strain
Stage & tissue

Cell Line
Recent Updates
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FB2013_03
FB2013_02
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Description & Members
Description	A set of isogenic deficiency stocks created by FLP-induced recombination between FRT-carrying transgenic insertions; molecularly defined deletion endpoints correspond to initial location of the progenitor insertions. Initial core set of 209 isogenic deletions provides ~60% euchromatic genome coverage. (Ryder et al., 2007)
Parent collections
Component collection(s)
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector	P{RS3} (Ryder et al., 2004) P{RS3r} (Ryder et al., 2004) P{RS5} (Ryder et al., 2004) P{RS5r} (Ryder et al., 2004)
Sample preparation	Deletion-generation strategy made use of extensive collection of ~3300 isogenic FRT-carrying transgenic insertion lines (FBrf0179424); all lines were mapped by inverse PCR. (Ryder et al., 2007) Progenitor stocks were isogenic FRT-carrying transgenic insertion lines, using insertions of P{RS3} and P{RS5}. Initially, internal recombination mediated by FLP recombinase between the FRT sites in P{RS3} and P{RS5} was induced (flip-out), to produce the remnant form of these elements, P{RS3r} and P{RS5r}, each of which has a nonfunctional white gene and a single FRT site. The flip-out recombination event was extremely efficient, over 98%. (Ryder et al., 2004)
Collection preparation	Recombination between FRT elements in two insertions in the appropriate relative orientation results in deletion of the genomic region between the insertions and production of a hybrid element that contains one FRT element at the recombination point (FBrf0091061). FLP-mediated recombination between P{RS3r} and P{RS5r} elements (flip-in) in trans and in the appropriate orientation produced a hybrid P-element with two 3' ends, a reconstituted functional miniwhite gene, and a deletion of the intervening genomic region. The efficiency of the flip-in event varied with the size of the deletion produced. (Ryder et al., 2004) The pilot experiment described in FBrf0179424 was scaled up. Deletion endpoints were confirmed by PCR (with primers within the predicted flanking genomic DNA and/or within the residual P-element at the recombination point), by genetic complementation, or by both. (Ryder et al., 2007)
Mode of assay
Assay platform
Data analysis	Of 870 different deletions that were attempted, 665 (76%) were recovered. This set covers ~77% of the euchromatic genome; average size of 368kb; average of 44 genes uncovered. Of the 209 deletions in the core collection, 89% have been confirmed by PCR, 64% confirmed by genetic complementation, and 54% by both methods. (Ryder et al., 2007) To confirm the stability of the double 3′ P-elements, the loss of the miniwhite marker in the presence of P-transposase was assayed for 3 deletion lines; no miniwhite[-] progeny were observed. (Ryder et al., 2004)
Additional data
	More information is available under: DrosDel Aberration.dataset.DrosDel.2012.8.8.xlsx
Associated files	Aberration.dataset.DrosDel.2012.8.8.xlsx (Millburn et al., 2012.8.1)
Additional sites
Synonyms & Secondary IDs
Reported As
Symbol Synonym	Dfs_DrosDel_set1 DrosDel Dfs
Secondary FlyBase IDs

References ( 3 )
Research paper	Ryder et al., 2007, Genetics 177(1): 615--629 The DrosDel deletion collection: a Drosophila genomewide chromosomal deficiency resource. [FBrf0202170] Ryder et al., 2004, Genetics 167(2): 797--813 The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster. [FBrf0179424]
FlyBase analysis	Millburn et al., 2012.8.1, Lines in aberration datasets (files on ftp site). Lines in aberration datasets (files on ftp site). [FBrf0219195]