Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1306543 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:we applied RNA-seq to detect novel expressed transcripts in 12 tissues of giant pandas, using a transcriptome reconstruction strategy combining reference-based and de novo methods. Then we used mass spectrometry method to identify proteomes of five selected tissues, aiming at validating these novel full-length genes we identified.
2015-12-23 | PXD002917 | Pride
Project description:Rhododendron fortunei Transcriptome or Gene expression
| PRJNA216973 | ENA
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>
2019-05-07 | MTBLS855 | MetaboLights
Project description:<div>Olive (<i>Olea europaea</i>) 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><b><br></b></div><div><b>Polyphenols UPLC-MS</b> protocols and data are reported in the current study <b>MTBLS814</b>.</div><div><br></div><div><b>GC-MS</b> protocols and data associated to this study are reported in <b><a href="https://www.ebi.ac.uk/metabolights/MTBLS855">MTBLS855</a></b>.</div><div><br></div><div><span _ngcontent-iov-c3="" class="ng-star-inserted"><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="https://www.ebi.ac.uk/metabolights/MTBLS1127">MTBLS1127</a>.</b></span></span></div><div><br></div><div><br></div>
2019-05-07 | MTBLS814 | MetaboLights
Project description:Deregulated gene expression is a hallmark of cancer, however most studies to date have analyzed short-read RNA-sequencing data with inherent limitations. Here, we combine PacBio long-read isoform sequencing (Iso-Seq) and Illumina paired-end short read RNA sequencing to comprehensively survey the transcriptome of gastric cancer (GC), a leading cause of global cancer mortality. We performed full-length transcriptome analysis across 10 GC cell lines covering four major GC molecular subtypes (chromosomal unstable, Epstein-Barr positive, genome stable and microsatellite unstable). We identify 60,239 non-redundant full-length transcripts, of which >66% are novel compared to current transcriptome databases. Novel isoforms are more likely to be cell-line and subtype specific, expressed at lower levels with larger number of exons, with longer isoform/coding sequence lengths. Most novel isoforms utilize an alternate first exon, and compared to other alternative splicing categories are expressed at higher levels and exhibit higher variability. Collectively, we observe alternate promoter usage in 25% of detected genes, with the majority (84.2%) of known/novel promoter pairs exhibiting potential changes in their coding sequences. Mapping these alternate promoters to TCGA GC samples, we identify several cancer-associated isoforms, including novel variants of oncogenes. Tumor-specific transcript isoforms tend to alter protein coding sequences to a larger extent than other isoforms. Analysis of outcome data suggests that novel isoforms may impart additional prognostic information. Our results provide a rich resource of full-length transcriptome data for deeper studies of GC and other gastrointestinal malignancies.
2021-02-02 | PXD023373 | Pride
Project description:full-length RNA-seq of Arabidopsis (PRJCA018751)
| PRJDB38182 | ENA
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><span _ngcontent-ook-c3= class=ng-star-inserted><span _ngcontent-jcp-c3= class=ng-star-inserted><span _ngcontent-iov-c3= class=ng-star-inserted><b>Tyrosol only UPLC-MS</b> <span _ngcontent-iov-c3= class=ng-star-inserted>protocols and data associated to this study are reported in the current study</span></span></span></span><b><span _ngcontent-ook-c3= class=ng-star-inserted><span _ngcontent-jcp-c3= class=ng-star-inserted><span _ngcontent-iov-c3= class=ng-star-inserted><span _ngcontent-iov-c3= class=ng-star-inserted> MTBLS1127.<br></span></span></span></span></b></div><div><span _ngcontent-jcp-c3= class=ng-star-inserted><div><b><br></b></div><div><b>Polyphenols UPLC-MS</b> protocols and <span _ngcontent-ook-c3= class=ng-star-inserted><span _ngcontent-jcp-c3= class=ng-star-inserted>data associated to this study are reported in</span></span> <a href=https://www.ebi.ac.uk/metabolights/MTBLS814><b>MTBLS814</b></a>.</div><div><br></div><div><b>GC-MS</b> protocols and data associated to this study are reported in <b><a href=https://www.ebi.ac.uk/metabolights/MTBLS855>MTBLS855</a></b>.</div><div><br></div></span></div>
2019-07-26 | MTBLS1127 | MetaboLights