Fasting northern elephant seal pup blubber transcriptome

• Main Authors: Khudyakov, Jane, Martinez, Bridget, Crocker, Daniel, Ortiz, Rudy, Gemmell, Neil, Rutherford, Kim
• Format: Dataset
• Language: unknown
• Published: figshare 2018
• Subjects: 60802 Animal Cell and Molecular Biology; FOS Biological sciences; 60603 Animal Physiology - Systems; 60303 Biological Adaptation; 60604 Comparative Physiology; 60405 Gene Expression incl. Microarray and other genome-wide approaches; Nes; Nes’; Elephant Seal
• Online Access: https://dx.doi.org/10.6084/m9.figshare.5746227.v1; https://figshare.com/articles/Fasting_northern_elephant_seal_pup_blubber_transcriptome/5746227/1

De novo Trinity transcriptome assembly from blubber (adipose tissue) collected from weaned northern elephant seal (Mirounga angustirostris, NES) pups during their post-weaning fast. Samples were collected from independent cohorts of 6 pups each, "early fasting" (1-2 weeks post weaning) and "late fasting" (6-8 weeks post weaning) and total RNA was isolated (RIN: 7.6-9.0). Twelve strand-specific libraries were prepared according to Illumina protocol with Ribo-zero depletion (human/rat/mouse), and sequenced (125 bp paired-end reads) on one lane of Illumina HiSeq 2000, producing an average of 41.5 million reads per sample. De novo assembly was conducted using all 12 samples and Trinity v2.1.1 with default settings, including adapter trimming ,but without abundance normalization. The assembly contains 1,830,330 transcripts (contigs) in 1,635,200 gene clusters with mean and median contig length of 835 bp and 425 bp, respectively. Mapping rate of reads to assembly was 87% and the assembly contains 81.2% complete, 36.3% duplicated, and 15.5% fragmented vertebrate BUSCOs, with only 3.2% missing from this dataset. The assembly was annotated by BLASTx using DIAMOND v0.8.31 with "very sensitive" option against the UniProt/SwissProt database (downloaded 8/20/17), with e-value threshold of 0.001. We identified 389,363 homologs in the transcriptome. The raw assembly file is called FastingNESPupTrinityAssembly.gz and the annotation file is called FastingNESPupAssemblyAnnotation.xlsx (also available as a tab delimited text file).