Haplotype-specific expression of the sepiapterin reductase (SPR) gene based on RNA-seq data from throat skin collected from within the main color patch for a Uta stansburiana: Blue throat-color morph
The focal tissue was throat skin from the main color patch on the throat.  RNA was extracted using a New England Biolabs Monarch Total RNA Miniprep kit.  Libraries were prepared with a KAPA (Roche) stranded mRNA-Seq Kit with unique dual indexes.  The sequence data was cleaned with HTStream and mapped with STAR to the Uta stansburiana orange-morph genome that was modified as follows.  The sequence for the SPR coding sequence, untranslated regions (UTRs), and the divergent region upstream of the SPR gene were deleted from the orange-morph reference genome.  Then an orange (O) and blue (B) haplotype were added as separate contigs, each of which included the divergent upstream region, the 5' UTR, and most of the first exon of the SPR gene.The bam file includes the data for the O and B-haplotypes that were added in as separate contigs.  The expression of the SPR gene was compared between the O and B-haplotypes in a region including the 5' UTR, and most of the first exon of the SPR gene.  For this individual, the O and B-haplotypes were the exact haplotypes sequenced in this individual. The expression of the SPR gene was quantified in the region from 10283-10983 bp in the blue haplotype and from 7844-8544 bp in the orange haplotype.