Sisymbrium irio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA202979 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Resistance to the phenoxy synthetic auxin herbicide 2,4-D is conferred by a deletion mutation in the degron tail of IAA2. An RNA-Seq experiment was used to assemble a reference transcriptome for the weed species Sisymbrium orientale, to quantify gene expression, and to identify sequence variants in the alignments. A 27 bp deletion was identified in the IAA2 gene. Forward genetics supported the role of this deletion mutation in resistance. The IAA2 deletion allele was transformed into Arabidopsis thaliana to confirm that it conferred 2,4-D resistance.
2020-10-08 | GSE159202 | GEO
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Glucosinolates (GSLs) from Sysimbrium officinale and S. orientale were analyzed qualitatively and quantitatively by their desulfo-counterparts using UHPLC-DAD-MS/MS. Eight GSLs were identified in S. officinale, including Val-derived (glucoputranjivin) and Trp-derived (4-hydroxyglucobrassicin, glucobrassicin, 4-methoxyglucobrassicin, and neoglucobrassicin) as the major ones followed by Leu-derived (Isobutyl GSL), Ile-derived (glucocochlearin) and Phe/Tyr-derived (glucosinalbin). Different S. orientale plant parts contained six GSLs, with Met-derived (progoitrin, epiprogoitrin, and gluconapin) and homoPhe-derived (gluconasturtiin) as the major ones, followed by glucosinalbin and neoglucobrassicin. GSL breakdown products obtained by hydrodistillation (HD) and microwave-assisted distillation from S. officinale, as well as isopropyl isothiocyanate, as the major volatile in both isolates, were tested for their cytotoxic activity using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Generally, all volatile isolates showed similar activity toward the three cancer cell lines. The best activity was shown by isopropyl isothiocyanate at a concentration of 100 µg/mL after 72 h of incubation, with 53.18% for MDA-MB-231, 56.61% for A549, and 60.02% for the T24 cell line.
| S-EPMC9736730 | biostudies-literature
Project description:Genome-wide transcriptome sequencing at different stages of Drosophila melanogaster development, RNA-seq
2020-07-22 | E-GEOD-18068 | ExpressionAtlas
Project description:The complete chloroplast genome of Sisymbrium irio was determined. The length of the complete chloroplast genome is 154,001 bp. The whole chloroplast genome consists of 83,891 bp long single copy (LSC) and 17,630 bp small single copy (SSC) regions, separated by a pair of 26,240 bp inverted repeat (IR) regions. The S. irio chloroplast genome encodes 112 annotated known unique genes including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic position of S. irio is sister to Brassiceae and Thlaspideae.
| S-EPMC7799896 | biostudies-literature
Project description:Sisymbrium altissimum (S. altissimum), belonging to the family Brassicaceae, can grow in soils of all textures, even sand. Here, we reported the complete chloroplast (cp) genome of S. altissimum using Illumina sequencing data. The cp genome exhibited a typical quadripartite cycle of 154,042 bp, composing of a pair of inverted repeats (IRs, 26,260 bp) separated by a large single-copy (LSC, 83,912 bp) region and a small single copy (SSC, 17,610 bp) region. A total of 132 genes (87 protein-coding genes, 37 tRNAs, and eight rRNAs) were annotated in this cp genome. Phylogenetic analysis revealed that S. altissimum was closely related to Sisymbrium irio.
| S-EPMC8386710 | biostudies-literature
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11830 | biostudies-arrayexpress
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11831 | biostudies-arrayexpress