Chaetoceros decipiens (UNC1416) reference transcriptome

<p>Reference transcriptome and associated annotations for&nbsp;<em>Chaetoceros decipiens&nbsp;</em>(UNC1416).&nbsp;</p> <p>A culture was grown into late exponential phase for filtration. Total RNA was extracted using the RNAqueous-4PCR Total RNA Isolation Kit (Ambion, Foster City, CA, USA) according to the manufacturer&rsquo;s protocol with an initial bead beating step to disrupt cells. RNA libraries were created with either the Illumina TruSeq Stranded mRNA Library Preparation Kit. The library was&nbsp;sequenced on an Illumina MiSeq (300 bp, paired-end reads) and an Illumina HiSeq 2500 with one lane in high output mode (100 bp, paired-end reads) and another lane in rapid run mode (150 bp, paired-end reads).</p> <p>Raw reads were trimmed for quality with Trimmomatic v0.36 then assembled <em>de novo </em>with Trinity v2.5.1 with the default parameters for paired-reads and a minimum contig length of 90 bp. Contigs were clustered based on 99% similarity using CD-HIT-EST v4.7 and then protein sequences were predicted with GeneMark S-T.&nbsp;Protein sequences were annotated by best-homology (lowest E-value) with the KEGG (Release 86.0), UniProt (Release 2018_03), and PhyloDB (v1.076)&nbsp;databases via BLASTP v2.7.1 (E-value &le; 10^-5) and with Pfam 31.0&nbsp;via HMMER v3.1b2 (Dataset S2). KEGG Ortholog (KO) annotations were assigned from the top hit with a KO annotation from the top 10 hits (<a href="https://github.com/ctberthiaume/keggannot">https://github.com/ctberthiaume/keggannot</a>).</p> <p>Provided here are predicted proteins as nucleotides and peptides. Raw reads are deposited in SRA (SRP234548).</p>