Project description:Global metaproteomic analyses of microbial biomass from the upper water column of the Central Pacific Ocean. This dataset was used as a discovery dataset to identify peptide biomarkers for cyanobacterial populations for use in targeted metaproteomic calibrated multiple reaction monitoring (MRM) analyses published in in Saito et al., 2014 and 2015. Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., and Lamborg, C. H.: Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers, Science, 345, 1173-1177, 2014. Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M., Rappé, M. S., DiTullio, G., and Moran, D.: Needles in the Blue Sea: Sub‐Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome, PROTEOMICS, 15, 3521-3531, 2015.
Project description:This experiment was annotated by TAIR (http://arabidopsis.org). Col-0 suspension cells provided by Dr. C. Koncz and Dr. M. Umeda. 15 ml of Arabidopsis Col-0 suspension cells (Mathur et al. 1998) was transferred to 35 ml of a fresh modified Murashige and Skoog (MS) medium supplemented with 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose every 7 day, and cultured on a rotary shaker at 120 rpm in the dark at 22 C for subculture. For xylem vessel element induction, a 7.5 ml aliquot of 7-day-old subcultured cells was transferred into 42.5 ml of fresh medium that included 1 uM brassinolide and 10 mM H3BO3, and cultured as described above. The frequency of xylem vessel element formation was calculated as the proportion of xylem vessel elements to the number of living cells and the vessel elements. Experimenter name = Hiroo Fukuda Experimenter phone = +81-3-5841-4463 Experimenter fax = +81-3-5841-4462 Experimenter department = H Fukuda Laboratory Experimenter institute = University of Tokyo Experimenter address = Department of Biological Science Experimenter address = 2nd Buil. Experimenter address = Hongo 7-3-1, Bunkyo-ku Experimenter zip/postal_code = Tokyo 113-0033 Experimenter country = Tokyo Keywords: compound_treatment_design; time_series_design;
Project description:Synthetic peptides are commonly used in biomedical science for many applications in basic and translational research. Here, we assembled a large dataset of synthetic peptides whose identity was validated using mass spectrometry. We analyzed the mass spectra and used them for method validation as well as the creation of ground truth datasets and cognate databases. Contact: Michele Mishto, Head of the research group Molecular Immunology at King’s College London and the Francis Crick Institute, London (UK). Email: michele.mishto@kcl.ac.uk,
Project description:Global metaproteomic analyses of microbial biomass from the upper water column of the Central Pacific Ocean. This dataset was used as a discovery dataset to identify peptide biomarkers for cyanobacterial populations for use in targeted metaproteomic calibrated multiple reaction monitoring (MRM) analyses published in in Saito et al., 2014 and 2015. Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., and Lamborg, C. H.: Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers, Science, 345, 1173-1177, 2014. Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M., Rappé, M. S., DiTullio, G., and Moran, D.: Needles in the Blue Sea: Sub?Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome, PROTEOMICS, 15, 3521-3531, 2015.
Project description:Initial single 2fold probe was designed at the Landegren lab in Uppsala University, and the following experiments were performed at the Broad Institute at the Mikkelsen lab.
Project description:This experiment was annotated by TAIR (http://arabidopsis.org). Col-0 suspension cells provided by Dr. C. Koncz and Dr. M. Umeda. 15 ml of Arabidopsis Col-0 suspension cells (Mathur et al. 1998) was transferred to 35 ml of a fresh modified Murashige and Skoog (MS) medium supplemented with 1 ug /ml 2,4-dichlorphenoxyacetic acid and 3% sucrose every 7 day, and cultured on a rotary shaker at 120 rpm in the dark at 22 C for subculture. For xylem vessel element induction, a 7.5 ml aliquot of 7-day-old subcultured cells was transferred into 42.5 ml of fresh medium that included 1 uM brassinolide and 10 mM H3BO3, and cultured as described above. The frequency of xylem vessel element formation was calculated as the proportion of xylem vessel elements to the number of living cells and the vessel elements. Experimenter name = Hiroo Fukuda; Experimenter phone = +81-3-5841-4463; Experimenter fax = +81-3-5841-4462; Experimenter department = H Fukuda Laboratory; Experimenter institute = University of Tokyo; Experimenter address = Department of Biological Science; Experimenter address = 2nd Buil. Experimenter address = Hongo 7-3-1, Bunkyo-ku; Experimenter zip/postal_code = Tokyo 113-0033; Experimenter country = Tokyo Experiment Overall Design: 12 samples were used in this experiment
Project description:The Aging, Dementia and Traumatic Brain Injury Study is a detailed neuropathologic, molecular and transcriptomic characterization of brains of control and TBI exposure cases from a unique aged population-based cohort from the Adult Changes in Thought (ACT) study. This study was developed by a consortium consisting of the University of Washington, Kaiser Permanente Washington Health Research Institute, and the Allen Institute for Brain Science, and was supported by the Paul G. Allen Family Foundation. This freely available resource (http://aging.brain-map.org/) presents a systematic and extensive data set of study participant metadata, quantitative histology and protein measurements of neuropathology, and RNA sequencing (RNA-seq) analysis of hippocampus and neocortex. Specific methodological details are available on the “Documentation” tab at http://aging.brain-map.org/. Included in this data set are normalized RNA-Seq FPKM files used for analysis in "Neuropathological and transcriptomic characteristics of the aged brain", published in eLife. Other processed data files as well as sample and donor meta-data and QC metrics are available at http://aging.brain-map.org/download/index Controlled access to raw data files is available via https://www.niagads.org/datasets/ng00059