Reference Report

Reference
Citation	Horn, Thomas, Schmidt, Esther, Pelz, Oliver (2011.11.16). GenomeRNAi reagent in FlyBase (Export to RIS)
FlyBase ID	FBrf0216883
Publication Type	Personal communication to FlyBase
PubMed ID
PubMed Abstract
Text of Personal Communication	I improved the mapping of our RNAi reagents (BKN/HD2 and HFA libraries) and wanted to provide you with this data. As you pointed out during your last E-Mail, the gene locations and chromosomal locations of RNAi reagents reported by NEXT-RNAi do not match in every case. This is not a bug, but NEXT-RNAi uses the mappings of potential siRNAs generated from the long dsRNA to define the primary RNAi target. In cases where no gene is annotated for the chromosomal target region, the dsRNA might still have short overlaps to other genes. NEXT-RNAi reports them as 'best targets', although they are not overlapping with the chromosomal target region. However, as you pointed out, this might be confusing. I now re-calculated the mapping in a simple 2-step approach (based on FlyBase r5.41): - I first mapped the RNAi reagent (using primer sequences) on the Drosophila genome using isPcr (in silico PCR from UCSC) - I then used these mappings to define the gene target (using gene mappings from the FlyBase gff file) For your report, I excluded all RNAi reagents that do have multiple chromosomal locations, target multiple gene (e.g. overlapping gene models) or target no gene at all. I generated a file in the format you requested: reagentID<tab>chromosomal_location<tab>FBgnID The file HD2_Mapping_r5.41.tab contains mappings for the BKN/HD2 library, the file HFA_Mapping_r5.41.tab for the HFA library. Would it be possible for you to replace the data you have by this new data? If you have questions or need further data (e.g. the primer sequences) please let me know.
DOI
Related Publication(s)
Research paper	Design and evaluation of genome-wide libraries for RNA interference screens. Horn et al., 2010, Genome Biol. 11(6): R61 [FBrf0214931]
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Associated Files	File date: 2011.11.17 ; File size: 4954030 ; File format: zip ; File name: RNAiLibs.zip
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Secondary IDs
Language of Publication	English
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Data from Reference
Genes (12)
	CG43773 CG43774 CG43775 CG43776 CG43777 CG43780 CG43781 CG44004 CG44005 CG44006 CG44014 CG44239
Libraries/Collections (2)
	HD2 HFA
Sequence features (31255)
	All Sequence features relating to this reference