Project description:This experiment aimed at indentifying secreted proteins/enzymes from saliva of the fly Pseudolycoriella hygida. To do this, twelve-day-old Psl. hygida larvae were selected and the last segment of the larvae was tied with elastane fishing line with the help of a stereomicroscope. This was performed to avoid contamination of saliva samples with feaces. Groups of 20 tied larvae were transferred to 1.5-mL microtubes and a few holes were made in the microtube cap. Then, the microtubes were incubated at 22 °C for 3 h. After removing the larvae, the microtubes were briefly centrifuged at 15,000 g for 30 s, and the secreted saliva, usually 2-3 ul per tube, was stored at -20 °C until gel electrophoresis.
Project description:We classified samples and deciphered a key genes signature of intratumor heterogeneity by Principal Component Analysis and Weighted Gene Co-expression Network Analysis. At the genome level, we identified common GB copy number alterations and but a strong inter-individual molecular heterogeneity.
Project description:To identify substrates of the ubiquitinating E3 enzyme Rsp5 we applied purified Rsp5 to duplicate protein arrays. The Rsp proteins were expressed as fusion proteins to GST. We used as a control Ubr1, a RING domain containing E3 ligase We analyzed Rsp5 from S.cerevisiae on duplicate arrays, with four control chips, two without Rsp5 and two with Ubr1.
Project description:Multi-omic absolute quantitative analysis of the yeast (Saccharomyces cerevisiae) mitotic cell cycle. Transcriptomics (RNA-Seq), proteomics (SILAC/ iBAQ), phosphoproteomics (SILAC/ iBAQ, enrichment with TiO2), and untargeted metabolomics (Metabolon, Inc.) were performed, all in biological triplicate. Three sub-projects from this central project were generated, in order of priority: (1) growth on glucose (n= 30 samples) (2) growth on ethanol (n= 21) and (3) pheromone effect (n= 51 samples; combined glucose and ethanol samples). For each sample, every omic type was analysed (n=4; transcriptomic, proteomic, phosphoproteomic, and metabolomic). Total omic samples generated for project = 204.
Project description:- mRNA abundance from wild type grown in LB or M9 (mRNA vs. Genomic DNA) : GSM30231 - GSM30238, GSM30338-GSM30341 - mRNA abundance grown in LB with norfloxacin treatment for 10 min or 30 min (mRNA vs. Genomic DNA): GSM30247-GSM30262 - mRNA abundance from gyrA (D82G) mutant grown in LB (mRNA vs. Genomic DNA):GSM30239-GSM30246 - Transcription profile between wild type and gyrA (D82G) mutant: GSM30330-GSM30337
Project description:Plasma proteins were digested with trypsin and the resulting peptides were analyzed by nanoLC–MS/MS on an EASY-nLC 1200 system coupled to an Orbitrap Exploris 480 mass spectrometer. Peptides were loaded onto a self-packed C18 reversed-phase column (25 cm × 100 μm i.d.) and separated at 500 nL/min using a linear gradient with solvent A (0.1% formic acid, 2% acetonitrile in water) and solvent B (0.1% formic acid, 90% acetonitrile in water): 4–20% B (0–68 min), 20–32% B (68–82 min), 32–80% B (82–86 min), and 80% B wash (86–90 min). The MS was operated with FAIMS using compensation voltages of −70 V and −45 V. Full MS scans were acquired at 60,000 resolution over m/z 400–1,200, and MS/MS scans at 30,000 resolution (first mass m/z 110). The top 15 precursors were selected for HCD (NCE 27%) with 30 s dynamic exclusion; AGC target was 75%, intensity threshold 10,000 ions/s, and maximum injection time 100 ms. TurboTMT was disabled for label-free quantification. Raw data were processed in Proteome Discoverer v2.4.1.15 and searched against the Homo_sapiens_9606_PR_20201214.fasta database (75,777 entries) with a reverse decoy strategy. Trypsin was specified with up to two missed cleavages; minimum peptide length was 6 aa. Carbamidomethyl (C) was set as a fixed modification; oxidation (M), protein N-terminal acetylation, methionine loss, and methionine loss + acetylation were set as variable modifications (≤3 variable modifications per peptide). Precursor and fragment mass tolerances were 10 ppm and 0.02 Da, respectively. FDR was controlled at <1% at the PSM, peptide, and protein levels. For label-free quantification, peptide intensities were normalized by peptide-wise mean centering across samples followed by within-sample median normalization, and protein abundances were summarized as the median of normalized peptide values per protein for downstream analyses.
Project description:Relative quantification of protein abundances of three yeast strains (Saccharomyces cerevisiae CEN.PK113-7D, Kluyveromyces marxianus CBS6556 and Yarrowia lipolytica W29) cultivate in chemostats under different conditions. The conditions for Saccharomyces cerevisiae CEN.PK113-7D are: - Standard condition – 30°C, pH 5.5 - High temperature - 36°C, pH 5.5 - Low pH - 30°C, pH 3.5 - Osmotic stress – 30°C, pH 5.5, 1M KCl The conditions for Kluyveromyces marxianus CBS6556 are: - Standard condition – 30°C, pH 5.5 - High temperature - 40°C, pH 5.5 - Low pH - 30°C, pH 3.5 - Osmotic stress – 30°C, pH 5.5, 0.6 M KCl The conditions for Yarrowia lipolytica W29 are: - Standard condition - 28°C, pH 5.5 - High temperature - 32°C, pH 5.5 - Low pH - 28°C, pH 3.5 This study is part of the OMICS data generation of CHASSY project (European Union’s Horizon 2020 grant agreement No 720824).
Project description:This SuperSeries is composed of the following subset Series: GSE24037: Salivary cytokine alterations in HIV infection part 1 GSE24064: Salivary cytokine alterations in HIV infection part 2 Refer to individual Series
Project description:This SuperSeries is composed of the following subset Series: GSE32691: Autoantibody profile timecourse of UNK GSE32874: Personal Omics Profiling Reveals Dynamic Molecular Phenotypes and Actionable Medical Risks Refer to individual Series
Project description:Here we examine key regulatory pathways underlying the transition from compensated hypertrophy (HYP) to decompensated heart failure (HF) and sudden cardiac death (SCD) in a guinea pig model by integrated multi-ome analysis. Relative protein abundances from sham-operated, HYP and HF hearts were assessed by iTRAQ shotgun LC-MS/MS. Metabolites were quantified by LC-MS/MS or GC-MS. Transcriptome profiles were obtained using DNA microarrays. The guinea pig HF proteome exhibited classic biosignatures of cardiac HYP, left ventricular dysfunction, fibrosis, inflammation and extravasation. Fatty acid metabolism, mitochondrial transcription/translation factors, antioxidant enzymes, and other mitochondrial processes, were downregulated in HF, but not HYP. Proteins upregulated in HF implicate extracellular matrix remodeling, cytoskeletal remodeling, and acute phase inflammation markers. Among metabolites, downregulation of acyl-carnitines was observed in HYP, while fatty acids accumulated in HF. Correlation of transcript and protein changes in HF is weak (R2=0.23), suggesting transcript/proteome divergence may reveal post-transcriptional gene regulation in HF. Proteome/Metabolome integration suggests metabolic bottlenecks in fatty acyl-CoA processing by carnitine palmitoyl transferase (CPT1B) as well as TCA cycle inhibition. We present a model by which acute signaling in HF, including Ca2+ dysregulation and low cAMP levels, is coupled to mitochondrial metabolic and antioxidant defects, through a CREB/PGC1 transcriptional axis. Animal Model The guinea pig model of heart failure and sudden cardiac death has been described previously. Briefly, the HF and SCD guinea pig model was produced by combining ascending aortic constriction (AC) and daily isoproterenol challenge (ACi model). Specifically, Hartley guinea pigs (~250 g; Hilltop Lab Animals) were anesthetized with 4% isoflurane in a closed box for 4min, and then intubated and ventilated with oxygen and 2% isoflurane. Ascending aortic constriction (AC) was produced by tying a suture around the ascending aorta using an 18‐gauge needle as a spacer, which was then removed. For sham operations the procedure was identical though the suture was not tied. After the procedure, bupronex (0.05 mg/kg) was administered via intramuscular injection for analgesia and animals were observed until full recovery. Isoproterenol was administered daily by intra peritoneal injection at 1 mg/kg for the first week after surgery and at 2 mg/kg for a subsequent 3 weeks. As characterized previously (1), cardiac function of ACi animal is well compensated in the first 2 weeks (HYP) but declined rapidly thereafter (HF). Hypertrophic heart was collected between 1-2 weeks post-surgery (ACi-2w), whereas failing heart was collected at 4 weeks after surgery (ACi-4w). Following retrograde perfusion with 20ml Tyrode’s solution, excised hearts were Snap-frozen in liquid N2 and stored at -80°C Experimental Design The experiment consisted of 3 treatment groups: 1) HYP (ACi-2wk), 2) HF (ACi-4wk) 3) sham-operated animals with daily administration for 4 weeks (Shami-4w). 1 heart from each group was included in an iTRAQ 4-plex experiment wherein peptides from each heart are subjected to reaction with an isobaric label. The experiment was repeated twice, yielding a total of 3 independent experiments quantifying the peptides from 9 hearts. ITRAQ reagents were shuffled among treatment groups for each experiment to minimize labeling bias.