Project description:Excerpt from a larger study which characterized the transcriptional effects of a spinal cord contusion injury in rats. This is the data from the almost chronic contusion state (35 days) at the injury site (Thoracic 8) - where we saw significant changes in several areas, including cholesterol metabolism genes. Other spinal cord areas (rostral, caudal) and time-points (3 hours, 24 hours, 7 days and 35 days) were analyzed as well and are discussed in our paper and at www.crpf.org/microarray.
Project description:Previously, we published a dataset of human blood plasma and serum samples of 10 healthy males and 10 healthy females, fractionated on a set of sorbents (cation exchange Toyopearl CM-650M, CM Bio-Gel A, SP Sephadex C-25 and anion exchange QAE Sephadex A-25) and analyzed by LC-MS/MS individually and pooled in equal amounts (Supplementary Table S1, Sheet 1) [33]. The mass spectrometry peptidomics data was deposited to the ProteomeXchange Consortium via the PRIDE partner repository (dataset identifiers PXD008141 and 10.6019/PXD008141). Direct download link: http://www.ebi.ac.uk/pride/archive/projects/PXD008141. We analyzed this dataset again within this work. The detailed information about the dataset of blood plasma/serum samples of 20 healthy donors fractionated on a set of sorbents is available in the original paper [33], including the clinical parameters of the donors, sample collection, plasma/serum fractionation, peptide extraction and LC-MS/MS analysis. 33. Arapidi, G. et al. Peptidomics dataset: Blood plasma and serum samples of healthy donors fractionated on a set of chromatography sorbents. Data Brief 18, 1204–1211 (2018).
Project description:This dataset contains raw mass spectrometry data (in the form of Thermo Fisher .RAW files) supporting associated publication “Variable blood processing procedures contribute to plasma proteomic variability” by Halvey et al.
The experiments characterized by these data evaluated effects on human plasma proteome of processing delay (from blood draw to the first centrifugation: 0, 6, 24, 48, 72 and 144 hours) and the type of anticoagulant tube used for blood collection (heparin or EDTA). Sample names indicate combinations of corresponding conditions - e.g. 48h_hep = 48 hours in heparin tube.
For the “6h_EDTA” experiment there were several instances of LC-MS/MS analytical replicates for this sample. It should be noted that for this experiment the .RAW file from the “./updates/2020-08-03_vfarutin_60de013e/raw/” folder under this dataset FTP address represents the actual LC-MS/MS run used to generate the data in the associated paper by Halvey et al.
Project description:This dataset contains raw mass spectrometry data (in the form of Thermo Fisher .RAW files) supporting associated publication “Variable blood processing procedures contribute to plasma proteomic variability” by Halvey et al.
The experiments characterized by these data evaluated effects on human plasma proteome of the following centrifugation parameters: number of spins (1 or 2), brake application (brake or no brake) and the speed of spin (1000g or 2000g). Conditions 1 through 8 correspond to following combinations of these factors - Condition 1: 1 spin 1000g no brake; Condition 2: 1 spin 1000g brake; Condition 3: 2 spins 1000g no brake; Condition 4: 2 spins 1000g brake; Condition 5: 1 spin 2000g no brake; Condition 6: 1 spin 2000g brake; Condition 7: 2 spins 2000g no brake; Condition 8: 2 spins 2000g brake.
For the experiments investigating Conditions 1 and 4 there were several instances of LC-MS/MS analytical replicates for each individual sample. It should be noted that for these two experiments the corresponding .RAW files from the “./updates/2020-08-03_vfarutin_3259f343/raw/” folder under this dataset FTP address represent the actual LC-MS/MS runs used to generate the data in the associated paper by Halvey et al.
Project description:In this study 3 pooling experiments were performed. In each of the 3 cohorts, a 'case' and a 'control' blood pool was compared - the goal being to identify single nucleotide polymorphisms with significantly different estimated pooling allele frequencies between cases and controls. For cohort 1, 100 individuals with blue eye color were placed in one pool (the 'control' pool) and 100 individuals with brown eye color were placed in another pool ( the 'case' pool). In cohort 2, 131 individuals with age-related macular degeneration were placed in one pool, with 216 control individuals in another pool. In cohort 3, 100 individuals with pseudoexfoliation syndrome were placed in a case pool - in this case the cohort 2 control sample was used as 'controls'. The blue/brown pools were hybridized to Illumina HumanHap550 arrays. The cohort 2 and 3 pools were hybridized to Illumina 1M arrays. After processing, the raw data are summarized to give pooling allele frequency estimates for each pool. The abstract from the paper describing these data is as follows: Genome-wide association studies (GWAS) have now successfully identified important genetic variants associated with many human traits and diseases. The high cost of genotyping arrays in large datasets remains the major barrier to wider utilization of GWAS. We have developed a novel method in which whole blood from cases and controls respectively is pooled prior to DNA extraction for genotyping. We demonstrate proof of principle by clearly identifying the associated variants for eye color, age-related macular degeneration and pseudoexfoliation syndrome in cohorts not previously studied. Blood pooling has the potential to reduce GWAS cost by several orders of magnitude and dramatically shorten gene discovery time. This method has profound implications for translation of modern genetic approaches to a multitude of diseases and traits yet to be analysed by GWAS, and will enable developing nations to participate in GWAS.
2009-08-08 | GSE17557 | GEO
Project description:Resequencing data of paper mulberry
Project description:Interventions: FOBT with collection paper vs FOBT without collection paper
Primary outcome(s): - Attendance rate
Study Design: Randomized controlled trial, Open (masking not used), Active, Parallel
Project description:The data submitted is for the proteomics data published in the paper: A systematic evaluation of isolation techniques and freeze-thaw effects on plasma extracellular vesicle heterogeneity and subpopulation profiling