To study the impact of wheat streak mosaic virus on global gene expression in wheat curl mite, we generated a de novo transcriptome assembly using 50 x 50 paired end reads from the Illumina HiSeq 2500. Reads were assembled using Trinity (version 2.0.6) and contigs greater than 200 nt were retained. All assembled transcripts were annotated using the Trinotate pipeline using blastp searches against the Swiss-prot/Uni-Prot database, blastx searches against the Swiss-prot/Uni-Prot databases, HMM searches against the Pfam-A database, blastp searches against the non-redundant protein database, and signalP and tmHMM predictions. To reduce noise from low abundance transcripts not well supported by the data, we filtered the assembly to retain only those transcripts with TPM values >=0.5.
- Raw Trinity Assemblytxt
Raw trinity assembly obtained from wheat curl mite using 50 x 50 Illumina...
- Trinotate annotations for raw Trinity assemblyxlb
Trinotate results for raw wheat curl mite transcriptome assembly
- Blastp results versus non-redundant protein databasetxt
Blastp results for protein coding unigenes from raw Trinity transcriptome...
- Protein predictions for raw trinity transcriptome assembly (wheat curl mite)txt
Putative coding regions were predicted using Transdecoder. Default...
- Final trinity transcriptome assembly for wheat curl mitetxt
Transcripts less than 200 nt and transcripts with TPM values less than 0.5...
- Nucleotide coding regions for final transcriptome assembly for wheat curl mitetxt
Nucleotide sequences corresponding to coding regions from the final...
- Protein predictions for final transcriptome assembly (wheat curl mite)txt
Protein coding regions were predicted using Transdecoder. ORFs were...
- Trinotate annotations for final Trinity assembly (wheat curl mite)xlb
Trinotate results for final wheat curl mite transcritpome assembly. Blastp...
|Release Date|| |
Ag Data Commons
|Contact Name|| |
|Public Access Level|| |
|Program Code|| |
005:037 - Department of Agriculture - Research and Education
|Bureau Code|| |
005:18 - Agricultural Research Service