GNPS .raw and .mzXML files of lipidomics analysis of pooled human faeces samples
Ontology highlight
ABSTRACT: Thermo .raw and centroided .mzXML files of a lipidomics LC-MS analyses ran on a Thermo Q-exactive instrument.
Pooled sampled were extracted using our regular lipid extraction protocol and with an adapted protocol for lipid extraction on the rest fraction after polar extraction, both performed six-fold.
Project description:Thermo .raw and centroided .mzXML files of a lipidomics LC-MS analyses ran on a Thermo Q-exactive instrument.
Pooled sampled were extracted using our regular lipid extraction protocol and with an adapted protocol for lipid extraction on the rest fraction after polar extraction, both performed six-fold.
Project description:Protocols for bone protein extraction adapted for radiocarbon dating were compared for their capability of being used also for paleoproteomics applications. Eight extraction protocols were tested on modern and archaeological bones. Molecular characterization of the extracts was performed by shot-gun proteomics. The effect of each extraction protocol on species identification through database searchnig was evaluated.
2018-12-11 | PXD010775 | Pride
Project description:DNA extraction protocol for maize pollen
| PRJNA962933 | ENA
Project description:Optimisation of a DNA extraction protocol
Project description:The goal of this study was to test if lipid-based cell hashing worked in salamander species and to test how lipid-based hashing compared to demultiplexing samples based on species origin and single nucleotide polymorphisms (SNP). Spleens were taken from four animals in total: one adult Pleurodeles waltl (female, 23.5grams and 16.1cm snout-to-tail, strain: tgSceI(CAG:loxP-GFP-loxP-Cherry)Simon), one adult Pleurodeles waltl (male, 13.95g and 15.7cm, tgSceI(CAG:loxP-GFP-loxP-Cherry)Simon), one adult Notophthalmus (female, 4.45g and 10.6cm, WT), and one adult Notophthalmus (male, 3.55g and 10.2cm, WT). Samples were stained with CM304 (Pleurodeles female), CMO305 (Pleurodeles male), and CMO306 (pool of both Notophthalmus samples) as per 10x Genomics 3’ Cellplex labeling protocol (Demonstrated Protocol, CG000391). These samples were processed through the 10x Controller and with Cellranger 7.0 using a dual species reference. The sample origin was determined by lipid-based hashing and then compared to mapping rates to each species transcriptome and using SNP-based demultiplexing.
Project description:The Meu5 RNA-binding protein stabilises its targets during meiosis. To investigate the function of Meu5 we induced synchronous meiosis in wild type or meu5delta cells (using pat1 thermo-sensitive mutations), and measured mRNA levels at regular intervals.
Project description:Proteomic Analysis. The proteomic expression of CGMCC 6315 under different nutrient concentration conditions was investigated by isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics. The CGMCC 6315 was cultured in LB broth and 1/15LB broth as described above, after which the strains were collected by centrifugation at 10,000× g for 10 min at 4°C. Protein extraction, digestion, iTRAQ labeling and peptide fractionation were performed using the protocol described by Jin et al. 29. Protein identification was conducted using a LC-20AD nano-HPLC instrument (Shimadzu, Kyoto, Japan) equipped with a Q EXACTIVE tandem mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) for data-dependent acquisition detection by nano-electrospray ionization. The raw MS/MS data were converted into MGF format by the thermo scientific tool Proteome Discoverer, and the exported MGF files were searched using Mascot (version 2.3.02) against the selected database containing 7546 CGMCC 6315 coding genes. The IQuant software was used for quantitative analysis of the labeled peptides with isobaric tags. Fold changes of >1.7 with p-values <0.05 were used as a cut off for differentially regulated proteins.