Project description:Several studies have shown that negative and positive miRNA-mRNA correlations are symmetrically distributed. While negative correlations are consistent with a faster degradation of miRNA targets, the presence of positive correlations suggests bidirectional interactions between the two classes of molecules. However, a comprehensive study of miRNA and mRNA correlations is lacking. A homogeneous map of miRNA and mRNA relationships was obtained by multidimensional scaling (MDS) applied to a single matrix including both heterologous (miRNA-mRNA) and homologous (miRNA-miRNA and mRNA-mRNA) correlations. Liver samples were obtained from 4 patients with HBV-associated acute liver failure (ALF), 10 liver donors and 7 subjects who underwent hepatic resection for liver angioma. This dataset is part of the TransQST collection.
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:Quantitative proteomic analysis of undiluted human vitreous biopsies collected at the time of primary surgical repair of rhegmatogenous retinal detachment (RRD), comparing patients who later developed proliferative vitreoretinopathy (PVR; n=8) with matched RRD controls who did not (n=8). Vitreous samples were processed by S-Trap digestion, labeled with TMT 10-plex reagents, and analyzed by LC–MS/MS on a Thermo Q Exactive instrument (two TMT 10-plex sets, two LC-MS/MS injection replicates per set; four .raw files total). Identification and quantitation were performed using Mascot followed by the proteoQ R pipeline. The dataset comprises 879 quantified proteins after stringent contaminant filtering. The deposition is intended as a methodologically transparent reference dataset of the baseline RRD vitreous proteome for future meta-analyses.
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:Temporally restricted feeding is known to impact the circadian clock. This dataset shows the effects of temporally restricted feeding on the hepatic transcriptome. C57/B6 mice were entrained for two weeks to a temporally restricted feeding schedule. Food was made available only between ZT(CT)1 and ZT(CT)9. Mice were then released into constant darkness while food availability was still restricted and liver tissue was collected at the indicated timepoints on the second day in constant darkness. Total RNA was extracted and 5ug were submitted to the standard Affymetrix protocol for amplification, labeling and hybridization.
Project description:Temporally restricted feeding has a profound effect on the hepatic circadian clock. While the circadian clock is largely unaffected by by extensive fasting, many transcripts are known to be affected by a fasting paradigm. This dataset shows the effect of extensive fasting on dynamic gene expression in the liver C57/B6 mice were entrained to ad libitum feeding schedule for two weeks. They were then released into constant were food was withdrawn at CT16. On the second day in constant darkness tissue was collected at the indicated timepoints. Total RNA was extracted and 5ug of total RNA was used for the standard Affymetrix protocol of amplification, labeling and hybridization
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.
Project description:The species Campylobacter jejuni is naturally competent for DNA uptake; nevertheless, nonnaturally transformable strains do exist. For a subset of strains we previously showed that a periplasmic DNase, encoded by dns, inhibits natural transformation in C. jejuni. In the present study, genetic factors coding for DNase activity in absence of dns were identified. DNA arrays indicated that nonnaturally transformable dns-negative strains contain putative DNA/RNA non-specific endonucleases encoded by CJE0566 and CJE1441 of strain RM1221. These genes are located on C. jejuni integrated element 2 and 4. Expression of CJE0566 and CJE1441 from strain RM1221 and a homologous gene from strain 07479 in DNase-negative Escherichia coli and C. jejuni strains indicated that these genes code for DNases. Genetic transfer of the genes to a naturally transformable C. jejuni strain resulted in a decreased efficiency of natural transformation. Modelling suggests that the C. jejuni DNases belong to the Serratia nuclease family. Overall, the data indicate that the acquisition of prophage encoded DNA/RNA non-specific endonucleases inhibits the natural transformability of C. jejuni through hydrolysis of DNA. The genomic diversity of 15 naturally competent or nonnaturally transformable Campylobacter jejuni strains were examined by microarray-based comparative genomic indexing (CGI) analysis. The CGI analysis allowed the assessment of CDS content for each C. jejuni strain relative to the C. jejuni DNA microarray, which comprises ORFs from strains NCTC 11168, RM1221. ORFs were spotted in duplicate. Genomic DNA from strains NCTC 11168/RM1221 were used as a reference DNA and competitively hybridized with genomic DNA from each of the other C. jejuni strains. Two replicates for each strain were performed. Data normalization was performed as in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.