PMC:4502371 / 8373-9744 JSONTXT

{"project":"2_test","denotations":[{"id":"25917920-22388286-43299623","span":{"begin":236,"end":240},"obj":"22388286"},{"id":"25917920-19505943-43299624","span":{"begin":303,"end":307},"obj":"19505943"},{"id":"25917920-22728672-43299625","span":{"begin":413,"end":417},"obj":"22728672"},{"id":"25917920-21653522-43299626","span":{"begin":476,"end":480},"obj":"21653522"},{"id":"25917920-20110278-43299627","span":{"begin":510,"end":514},"obj":"20110278"}],"text":"Whole genome sequencing:\nThe genomes of the mutant strains after outcrossing twice against N2 were sequenced using Illumina sequencing. Sequences were aligned to the WS220 reference C. elegans genome with bowtie2 (Langmead and Salzberg 2012), variants called with the samtools/bcftools suite (Li et al. 2009), and effects on gene function predicted and variants filtered with snpEff and SnpSift (Cingolani et al. 2012). Further specific analyses used vcftools (Danecek et al. 2011), bedtools (Quinlan and Hall 2010), and custom scripts.\nAfter whole genome sequencing, we found a single deletion in the mua-3 gene, but no other mutations in the range of 9.8 Mb to 10.5 Mb for chromosome III. The mutation was also validated because the original strain was from the knockout consortium of C. elegans, where the mutations are generated by the UV/TMP method to create deletions. The new allele of mua-3(uy19) contains a 488-bp in-frame deletion that includes parts of the 30th and 31st exons and the short intron between them. The flanking sequences are as follows: 5′ end of the deletion: 5′-TGAGGAGAATGGATA-3′ and 3′ end of the deletion: 5′-CACCACAGTCCAGTC-3′. The deletion results in deletion of the following 131 amino acids:\nRCRCRNGYHD DDPAHPGHRC SFMINECDSS NLNDCDRNAN CIDTAGGYDC ACKAPYRDEG PPQSPGRICR LNECLNPNRN TCDRNADCRD LDYGYTCTCR HGFYDQSPNP QEPGRICIEF QQEEHIERVK V."}