Computational protocol: Characterization of Adult Transcriptomes from the Omnivorous Lady Beetle Coleomegilla maculata Fed Pollen or Insect Egg Diet

Similar protocols

Protocol publication

[…] Total RNA samples were shipped on dry ice to the University of Washington High-Throughput Genomics Center, WTC East, Suite 600, 2211 Elliott Ave., Seattle, WA 98121-1692. Illumina (Illumina, Inc., San Diego, CA, USA) RNA-seq library construction, 36 bp single end multiplex quality control library testing, and 76 bp paired end multiplex 4x sequencing was followed by Trinity (Broad Institute, MA) contiguous sequence assembly . Sequences were assembled by diet treatment (eggs only or pollen only) and as a combined group assembly. Assembled sequences were limited by request to >200nt. Assembled sequences were provided to the USDA ARS Genomics and Bioinformatics Research Unit (GBRU) in Stoneville, MS for further analysis. [...] Assembled sequences were analyzed by NCBI BLAST® (US National Library of Medicine) using the tBLASTx “search translated nucleotide database using a translated nucleotide query” (database accessed 22 May 2013). BLAST results were analyzed by diet treatment (eggs only or pollen only) and as a combined group. Spreadsheet results were sorted by Hit Score and only those sequences in the two treatment groups meeting the combined criteria of >500 nucleotide (nt) and E (expect) score

Pipeline specifications

Software tools Trinity, BLASTN, TBLASTX
Applications RNA-seq analysis, Nucleotide sequence alignment
Organisms Corymbia maculata