Similar protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.


Pipeline publication

[…] al set of predicted coding sequences comprised 11,312 open reading frames., Trypanosoma theileri was grown as above and total RNA was extracted using the Qiagen RNeasy kit. Isolated RNA was sequenced at the Beijing Genomics institute (; last accessed August 23, 2017) using two different approaches, a conventional TrueSeq protocol and a protocol designed to enrich for 3′ ends of mRNA messages (). The number of reads, read length, and insert size of each library are shown in supplementary table S1, Supplementary Material online. The raw reads were used to identify and quantify the polyadenylation and spliced-leader acceptor sites in the genome of T. theileri using the SLaP mapper () using the default settings. Raw RNASeq reads are available from EBI ArrayExpress under the accession number E-MTAB-5327., The conventional TruSeq reads above were also used to quantify the mRNA abundance for each predicted gene in the T. theileri genome. Prior to quantification, reads were subject to quality filtering using trimmomatic as described earlier. The quality filtered paired-end reads were then used to quantify the abundance of the predicted gene models using RSEM () utilizing the default program parameters. mRNA abundances in T. brucei were derived from EBI ArrayExpress E-MTAB-3335 and E-MTAB-5460., The annotated proteins for Trypanosoma brucei TREU927, T. congolense IL3000, T. cruzi CL Brenner Esmereldo-like, T. rangeli SC58, T. grayi ANR4, T. vivax Y486, Leishmania tarentolae ParrotTarII, L. major Friedlin, L. infantum JPCM5, L. mexicana MHOMGT2001U1103, L. donovani BPK282A1, L. braziliensis MHOMBR71973M2269, and Crithidia fasiculata CfCl were downloaded from TriTrypDb V8.0 (). The predicted proteins from Phytomonas EM1 and Phytomonas Hart1 were obtained from (). The predicted proteins from Phytomonas serpens were obtained from () and for Tryp […]

Pipeline specifications

Software tools SLaP mapper, Trimmomatic, RSEM
Databases ArrayExpress TriTrypDB
Diseases Infection