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Northern elephant seal blubber transcriptome assembly (repeated ACTH challenge)

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modified on 01.01.2019, 00:33
Juvenile northern elephant seals received once-daily injections of synthetic adrenocorticotropic hormone (ACTH) for four consecutive days. Blubber samples were collected from study animals immediately prior to and four hours after the first and fourth ACTH administrations. RNA was isolated from the inner, metabolically active half (closest to muscle) of each blubber sample from four study animals. cDNA libraries were sequenced as 100-bp paired end reads on the Illumina HiSeq 4000 (mean 27 million reads/sample) at UC Berkeley.

A single reference transcriptome was assembled de novo using Trinity v2.4.0 with default settings (file "Trinity.CSM.all.fasta") and XSEDE computational resources (PSC Bridges Large). The assembly contains 1,216,779 contigs, of which 370,178 were annotated by blastx using the UniProt database (e-value threshold 0.001; file "Trinity.CSM.all.annotation.m8"). 92% of sequencing reads could be mapped back to the assembly and it contains 85.8% complete vertebrate BUSCOs. Mean contig length was 670 bp.

The raw assembly was filtered using TransDecoder; the filtered assembly contains 266,916 in silico predicted proteins (file "Trinity.CSM.all.fasta.transdecoder.pep").