Project description:MIADB: a cumulative collection of 172 tandem mass spectrometry (MS/MS) of a vast array of monoterpene indole alkaloids. Samples were analyzed using an Agilent LC-MS system composed of an Agilent 1260 Infinity HPLC coupled to an Agilent 6530 ESI-Q-TOF-MS operating in positive mode. A Sunfire analytical C18 column (150 × 2.1 mm; i.d. 3.5 μm, Waters) was used, with a flow rate of 250 μL/min and a linear gradient from 5% B (A: H2O + 0.1% formic acid, B: MeOH) to 100% B over 30 min. ESI conditions were set with the capillary temperature at 320 °C, source voltage at 3.5 kV, and a sheath gas flow rate of 10 L/min. The divert valve was set to waste for the first 3 min. There were four scan events: positive MS, window from m/z 100−1200, then three data-dependent MS/MS scans of the first, second, and third most intense ions from the first scan event. MS/MS settings were three fixed collision energies (30, 50, and 70 eV), default charge of 1, minimum intensity of 5000 counts, and isolation width of m/z 2. In the positive-ion mode, purine C5H4N4 [M + H]+ ion (m/z 121.050873) and the hexakis(1H,1H,3H-tetrafluoropropoxy)-phosphazene C18H18F24N3O6P3 [M + H]+ ion (m/z 922.009 798) were used as internal lock masses. Full scans were acquired at a resolution of 11 000 (at m/z 922). A permanent MS/MS exclusion list criterion was set to prevent oversampling of the internal calibrant.
Project description:In this exploratory study, we used laser microdissection to extract dopaminergic neurons from 10 human SNpc samples obtained at autopsy in Parkinson’s disease patients and control subjects. Extracted RNA and proteins were identified by RNA sequencing and nano-LC-MS/MS, respectively, and the differential expression between Parkinson’s disease and control group was assessed.
Project description:The aim of this experiment was to compare gene expression in leaves and stems of narrow-leafed lupin (Lupinus angustifolius L.) using Illumina RNA sequencing. Total RNA was isolated from leaves and stems of five narrow-leafed lupin (Lupinus angustifolius L.) genotypes with contrasting alkaloid regulation, including an iucundus low-alkaloid line (83A:476), a bitter Iucundus line (P27255) and three Bryansk low-alkaloid lines carrying the Iucundus-type RAP2-7 allele: 95826 (Bryanskij-35), 95927 (Bryanskij-123) and 95928 (Bryanskij-237/83). Plants, in five replication per genotype, were grown under controlled conditions optimal for growth, and leaf and stem samples were collected at flowering stage.
Project description:The aim of this experiment was to obtain full length transcript sequences of genes expressed in leaves and stems of narrow-leafed lupin (Lupinus angustifolius L.) using PacBio Iso-Seq. Total RNA was isolated from leaves and stems of five narrow-leafed lupin (Lupinus angustifolius L.) genotypes with contrasting alkaloid regulation, including an iucundus low-alkaloid line (83A:476), a bitter Iucundus line (P27255) and three Bryansk low-alkaloid lines carrying the Iucundus-type RAP2-7 allele: 95826 (Bryanskij-35), 95927 (Bryanskij-123) and 95928 (Bryanskij-237/83). Plants, in five replicates per genotype, were grown under controlled conditions optimal for growth, and leaf and stem samples were collected at flowering stage. For each genotype and organ, total RNA from five biological replicates was pooled in equal amounts and used for PacBio Iso-Seq library preparation and sequencing.
Project description:Samples containing stable isotope-labeled internal standards added to plasma and liver samples. Standards were obtained from a mix of NIH standards representing nine metabolite classes and the QreSS kit from Cambridge Isotope Laboratories (MA, USA). The samples were chromatographically separated using hydrophilic interaction liquid chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) chemistries in separate injections. The LC system was coupled to an Agilent 6560 ion mobility quadrupole time of flight mass spectrometer (Agilent Technologies, CA, USA), and the standards were analyzed in both positive and negative ionization mode. The MS/MS data were acquired at collision energies of 10, 20, and 40eV using an all-ions fragmentation approach with frames alternating between high and low fragmentation using a mass range of 50-1500 m/z.
Project description:This dataset belongs to a set of three RNA-Seq experiments that were carried out to study the regulation of monoterpenoid indole alkaloid production in the medicinal plant Catharanthus roseus. For this dataset, C. roseus stems were dissected to separate the epidermis from the lower tissues. Leaves were dissected to obtain veins and veinless leaves. As controls, undissected leaves and stems were used. Three biological replicates were analyzed per sample.