ena-STUDY-European Bioinformatics Institute (EMBL-EBI) -18-08-2014-16:34:08:260-473
de novo and reference based assemblies of the transcriptome of Culicoides sonorensis
With the aim of helping the gene prediction and annotation process of the Culicoides sonorensis-derived KC cell genome, we have sequenced the transcriptomes of this cell line under 11 different conditions. With the purpose of boosting gene expression, the cell line was challenged with 10 different treatments (Prostagalndin E1, Prostaglandin A1, 20 Hydroxyecdysome, Staphylococcus aureus Lipoteichoic acid, E. coli Lipopolysaccharide, Polyinosinic:polycytidylic acid, Insulin, Transcription growth factor ß1, fMLP and heat-shock at 36 C) and a control. RNA was extracted from each treated cell culture and TrueSeq libraries were barcoded and sequenced on a single lane of the Illumina HiSeq 2000 platform using 100 bp paired-end reads. The transcriptomes were assembled de novo using Trinity, but also using the KC cell assembly as a reference genome with TopHat and Cufflinks. The number of genes in each of the transcriptomes is similar, ranging from 11317 to 11995, and the number of transcripts is also similar between the transcriptomes, 13419 to 14188, and higher than the number of genes, indicating the presence of some differential transcripts. The number of total genes in the merged transcriptome was 11568 and the number of transcripts increased to 17554. Of these, 12535 aligned to 8294 of the predicted genes from the KC cell genome assembly with an identity at DNA level greater than 90%.
With the aim of helping the gene prediction and annotation process of the Culicoides sonorensis-derived KC cell genome, we have sequenced the transcriptomes of this cell line under 11 different conditions. With the purpose of boosting gene expression, the cell line was challenged with 10 different treatments (Prostagalndin E1, Prostaglandin A1, 20 Hydroxyecdysome, Staphylococcus aureus Lipoteichoic acid, E. coli Lipopolysaccharide, Polyinosinic:polycytidylic acid, Insulin, Transcription growth factor ß1, fMLP and heat-shock at 36 C) and a control. RNA was extracted from each treated cell culture and TrueSeq libraries were barcoded and sequenced on a single lane of the Illumina HiSeq 2000 platform using 100 bp paired-end reads. The transcriptomes were assembled de novo using Trinity, but also using the KC cell assembly as a reference genome with TopHat and Cufflinks. The number of genes in each of the transcriptomes is similar, ranging from 11317 to 11995, and the number of transcripts is also similar between the transcriptomes, 13419 to 14188, and higher than the number of genes, indicating the presence of some differential transcripts. The number of total genes in the merged transcriptome was 11568 and the number of transcripts increased to 17554. Of these, 12535 aligned to 8294 of the predicted genes from the KC cell genome assembly with an identity at DNA level greater than 90%.