Multigenic Delineation of Lower Jaw Deformity in Triploid Atlantic Salmon (Salmo salar L.)

Lower jaw deformity (LJD) is a skeletal anomaly affecting farmed triploid Atlantic salmon (<i>Salmo salar</i> L.) which leads to considerable economic losses for industry and has animal welfare implications. The aim of this project was to delineate for the first time through transcriptome analysis differential gene expression in the jaw of fish affected by LJD (compared to normal fish) to detect genes which correlate with and may characterise LJD, allowing the description of possible mechanisms underlying the condition.<br>Lower jaw tissue of triploid Atlantic salmon individuals affected by LJD (<i>n</i> = 6) and phenotypically normal (Normal) (<i>n</i> = 6) were used. Equal amounts of RNA from three individuals from the same category were mixed to generate a total of four pooled samples representing two replicates of LJD and two replicates of Normal. <br>Samples were prepared for sequencing by the Australian Genome Research Facility (AGRF, Melbourne, Australia) according to the manufacturer’s instructions (Illumina, San Diego, CA, USA).<br>The files made available are sequencing data in BAM format of the four pooled samples mentioned above. The name of each file allows to easily identify which pooled sample each file corresponds to.<br><br> <br>

下颌畸形（Lower jaw deformity, LJD）是一种侵袭养殖三倍体大西洋鲑（*Salmo salar* L.）的骨骼发育异常病症，会为水产养殖业带来可观的经济损失，同时涉及动物福利相关问题。
本研究首次通过转录组分析（transcriptome analysis），对比患LJD的鲑鱼与正常个体的下颌组织差异基因表达（differential gene expression）情况，以筛选与LJD相关、可用于表征该病症的基因，从而阐明该病症潜在的发病机制。
本研究采集了6例患LJD的三倍体大西洋鲑下颌组织样本（*n*=6）与6例表型正常的个体样本（*n*=6）。将同一分组的3个个体的总RNA等量混合，最终获得4个混合样本，分别对应LJD组的2个生物学重复与正常组的2个生物学重复。
样本测序文库制备由澳大利亚基因组研究中心（Australian Genome Research Facility, AGRF，澳大利亚墨尔本）按照测序仪制造商Illumina（美国加利福尼亚州圣迭戈市）的标准操作指南完成。
本次公开提供的文件为上述4个混合样本的BAM格式测序数据，每个文件的文件名均可直观标识其对应的混合样本分组。