Project description:We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data. PacBio long reads and Illumina short reads were generated from the same hESC cell line H1. PacBio reads were error-corrected by Illumina reads to identify transcripts. rSeq is used to estimate gene/transcript abundance of the identified transcriptome.
Project description:PacBio SMRTseq long reads and Illumina short reads of pig testis, epididymis, vesicular gland, prostate gland, and bulbourethral gland
Project description:The goal of this study was to determine how an HIV quasispecies is maintained in the face of selection. We deep sequenced the HIV provirus from cell populations as well as single cells at different time points from in vitro evolution experiments and found that when a less fit and more fit infect the same cell, they share components (complmentation) and therefore allow the less fit to perpetuate. We reproduced a quasispecies to an HIV reverse transcriptase inhibitor. The drug resistant genotype never completely supplanted the drug sensitive genotype, which stabilized at about 20% of viral sequences. Single-cell sequencing showed that resistant genotype frequency plateaued when cells were co-infected with sensitive and resistant genotypes, suggesting a sharing of viral proteins in co-infected cells (complementation), masking genotypic differences. To test if complementation can confer phenotypic drug resistance, we co-transfected fluorescently labelled molecular clones of sensitive and resistant HIV and observed drug resistance in genotypically sensitive virus from co-transfected cells. Resistant virus preferentially co-infected cells with drug sensitive HIV, explaining initiation of co-infections. Modelling showed that a stable quasispecies could form at the experimental multiplicities of infection. Conclusions: Complementation can lead to a quasispecies in infection environments where multiple infections per cell are common
Project description:To assess compatibility in sequence analysis we compared results from Sanger sequencing (with sequencing threshold >15%) and Next Generation Sequencing (with sequencing treshold >5%). Totally, there were 60 patients included in this part of the study. Here we demonstrate how reliable tool for fast and accurate identification of low-level viral quasispecies is deep-sequencing.
Project description:Since short reads from Illumina RNA-seq data are challenging to map to repetitive elements , we wanted to confirm the bulk RNA-seq findings using an orthogonal method, namely, using the long read technology of Pacific Biosciences (PacBio) full-length transcriptome sequencing. This dataset provided around 1.1 (WT) and 1.3 (RBM4 KO) million sequence reads of 2.6 kb average length mapping to the human genome.
Project description:To assess compatibility in sequence analysis we compared results from Sanger sequencing (with sequencing threshold >15%) and Next Generation Sequencing (with sequencing treshold >5%). Totally, there were 48 patients included in this part of the study but sequencing for one sample failed. Here we demonstrate how reliable tool for fast and accurate identification of low-level viral quasispecies is deep-sequencing.
Project description:<div>Olive (Olea europaea) has a long history of medicinal and nutritional values own to it rich in polyphenol and fatty acids (FAs) in fruits. In order to better understand the biosynthesis important of these metabolites, we generated comprehensive Iso-Seq full-length and illumina RNA-seq transcriptome, and targeted metabolomics dataset of different olive fruits maturity. The targeted metabolomics by using both GC/MS and LC/MS were totally quantified 35 FAs and 13 polyphenols. Iso-Seq library was constructed and sequenced by PacBio Sequel System, and a total of 5,891,652 (10.55 G) with an average length of 1,791 subreads were obtained. 492,350 circular consensus sequences (CCSs) were formed after merging and error correction through subread comparison. Of the 492,350 CCSs, 399,263 were found to be full-length non chimera (FLNC) reads, and 187,517 consensus reads were finally obtained by using clustering algorithm of Iterative clustering for error (IEC). These multiomics data provide a foundation to elucidate the mechanisms regulating biosynthesis of polyphenol and FAs during the maturation of olive fruits.</div><div><br></div><div><div><b>GC-MS</b> protocols and data are reported in the current study <b>MTBLS855</b>.</div><div><br></div><div><span _ngcontent-jcp-c3="" class="ng-star-inserted"><b>Polyphenols UPLC-MS</b></span> protocols and data associated to this study are reported in <b><a href="http://www.ebi.ac.uk/metabolights/editor/study/MTBLS814">MTBLS814</a></b>.</div><div><br></div><div><b>Tyrosol only UPLC-MS</b> <span _ngcontent-iov-c3="" class="ng-star-inserted">protocols and data associated to this study are reported in <b><a href="http://www.ebi.ac.uk/metabolights/editor/study/MTBLS814"><a href="https://www.ebi.ac.uk/metabolights/MTBLS1127">MTBLS1127</a>.</a></b></span></div></div>
