Project description:Transcriptome analysis the genes expression in SsMYRV4-infected strain Ep-1PNA367T1 and SsMYRV4-free strain Ep-1PNA367. the two strains were grown on a cellophane membrane overlaid onto PDA medium at 20℃ for 3 days, samples were collected for total RNA extraction. The RNA samples were sequenced and anlysized by the BGI Co., Ltd. Total clean reads of each sample above 5000000.The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.

2017-02-07 | GSE94575 | GEO

Antiviral and anti-inflammatory properties of novel anti-HIV candidate ABX464 promotes specifics RNA splicing while preserving cellular RNA integrity.

Project description:Purpose: To ensure that ABX464 acted specifically on HIV splicing and did not significantly or globally affect the splicing events of human genes, we used an assembly approach of HIV (YU2 strain) putative transcripts and human long non-coding sequences from paired-reads (2x75bp) captured on a NimbleGen SeqCap® EZ Developer Library (Roche/NimbleGen). Methods: Cells were infected with 80 ng of p24/106 cells of the YU-2 strain for 4 to 6 hours and then rinsed with PBS before medium renewal, followed by high-throughput RNAseq from custom SeqCap EZ capture libraries. Each raw dataset of the samples contained between 5 and 30 million paired-end reads (75 bp), with an average of approximately 12 million raw reads per sample. Results: The raw reads were then cleaned and assembled per library to generate contigs, giving an average of 930 contigs per sample for further analyses. Conclusions: Our results show that high-throughput analyses coupled with bioinformatics-specific tools offers a comprehensive and more accurate view of mRNA splicing within a cell.

2018-12-31 | GSE120109 | GEO

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