For the purposes of the 1KP project, 30 μg of total RNA was requested for each taxon from BGI for a full transcriptome sequence (Johnson et al., 2012).
To access the GO classification for each gene, the full transcriptome sequences of A. ilicifolius and A. leucostachyus were annotated with the Swiss-Prot database in AgBase [ 17] with a cutoff e-value of 1e-6.
In the current study we chose to be conservative and included only those prokaryotic organisms that have a full transcriptome sequence available on GenBank, which limits us to 1,976 organisms.
IRG genes of the CIM mouse strain were sequenced via full transcriptome Illumina sequencing of IFNγ-induced diaphragm-derived cells (DDC, see below) in the Cologne Centre of Genomics (CCG).
The field of genomics is expanding rapidly with full genome and transcriptome sequencing of many model and non-model species.
This indicates that to approach full transcriptome information, the sequencing of both types of libraries is necessary.
To predict the repertoire of functions already visible from the currently assembled transcriptome, we compared it with the full transcriptome available from the sequencing effort on M. tardigradum ESTs and available data regarding prokaryotic COGs 38 and eukaryotic KOGs.
To prepare RNA for transcriptome sequencing, full-sibling replicate seeds from six families —three families each of those identified as the most/least resistant from the R/S selection lines were planted in 4-inch pots with Fafard 3B soil (Agawam, MA) and randomized in the greenhouse on June 3 , 2012
To establish the immune repertoire of C. floridanus the full transcriptome was analysed by Illumina sequencing, comparing challenged and unchallenged animals (pools of whole larvae L2 and workers W2 for each sample).
Note that while P. trichocarpa and S. bicolor are model species with full genome (and transcriptome) sequences, sequences from trees common in the ecology of the great tit (oak, ash, beech, hazel, sycamore) are not well represented in the RefSeq RNA database.
