Project description:Targeted LC/MS Metabolomics. Cecal contents were lyophilized overnight and approximately 2.5-5 mg was homogenized in 250 µL of 50% acidified acetonitrile (0.3% formic acid) for targeted LC/MS/MS metabolomics (acylcarnitines, amino acids, organic acids, nucleotides, and CoAs) according to validated, optimized protocols in our previously published study (Previs et al.). Separate aliquots of homogenates were extracted with solvents for each class of metabolites, and then each class was analyzed with a unique LC/MS/MS method to optimize their chromatographic resolution and sensitivity. Quantitation of metabolites in each assay module was achieved using multiple reaction monitoring of calibration solutions and study samples with isotopically-labelled internal standards on an Agilent 1290 Infinity UHPLC/6495 triple quadrupole mass spectrometer. Raw data was processed using Mass Hunter quantitative analysis software (Agilent). Calibration curves (R2 = 0.99 or greater) are either fitted with a linear or a quadratic curve with a 1/X or 1/X2 weighting. Metabolic and Proteomic Defects in Human Hypertrophic Cardiomyopathy Michael J. Previs, Thomas S. O’Leary, Neil B. Wood, Michael P. Morley, Brad Palmer, Martin LeWinter, Jaime Yob, Francis D. Pagani, Christopher Petucci, Min-Soo Kim, Kenneth B. Margulies, Zoltan Arany, Daniel P. Kelly, Sharlene M. Day bioRxiv 2021.08.18.455967; doi: https://doi.org/10.1101/2021.08.18.455967
Project description:<p>This dataset contains 10 Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) slides from cross-sections of surgically resected colorectal tissues with cancer and adjacent normal. The data is released with MassVision software platform for exploration and analysis of MSI data. Primary publication for citation: Jamzad et al., Analytical Chemistry 2025. Methods reference for acquisition conditions: Kaufmann et al., Metabolites 2023. Please cite BOTH papers when using this dataset, in whole or in part, in any publications or presentations.</p>
Project description:We asked how knockdown of genes associated with neurodegeneration using antisense oligonucleotides (ASO) affects disease phenotypes in an inducible TDP-43 transgenic mouse model (rNLS8, Walker et al., Acta Neuropathologica 2015) backcrossed to the C57BL/6 background. This dataset includes only the non-targeting control, which was also used as a replication cohort for transcriptional changes in rNLS8 mice (Rezaei et al., in revision at Nature Communications). We show cholesterol dysmetabolism and marker genes of disease-associated oligodendrocytes in the brain of rNLS8 mice. Data from mice receiving the targeting ASOs will be made available upon publication of the manuscript (Kocsis-Jutka et al, in preparation).
Project description:This ArrayExpress experiment contains RNA-seq data from human tissues, generated by Michael Snyder's lab at Stanford University as part of the ENCODE project ( https://www.encodeproject.org/search/?type=Experiment ). Sample information was obtained from the ENCODE data coordination center and protocol information was obtained from the associated publication in PNAS (Lin et al., 2014, PubMed ID 25413365). All samples, except for the ovary, were sequenced with technical replicates. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication. Technical replicates are marked in the âComment[technical replicate group]â column of sample-data-relationship format (SDRF) file for this record.
Project description:Analysis of in vivo antigen-specific (LCMV-specific, SMARTA TCR transgenic) follicular helper CD4 T cells (CXCR5high),versus non-follicular helper CD4 T cells (CXCR5low), eight days after viral infection. A paper including data analysis of these experiments has been accepted for publication (Robert J. Johnston et al. Bcl6 and Blimp-1 are reciprocal and antagonistic regulators of follicular helper CD4 T cell differentiation).
Project description:Construction of Parallel analysis of RNA ends (PARE) libraries was done as described by German et al., 2009. Raw reads consisting of short sequences of 16 to 21 nts after MmeI digestion.
Project description:Samples of the model lichen Ramalina farinacea were collected from six sites (countries) across a geographical gradient in Europe: Czech Republic, Estonia, Finland, Norway, Spain, and Sweden. Sampling was carried out in winter (January-March 2023) and summer (June-July 2023), with six individuals collected per site and season. Metabolites were extracted and derivatized according to a protocol for plant samples (Lisec et al., 2006), with major modifications. Briefly, methanol extracts from dry samples were obtained by grinding and 70ºC incubation. Extracts were vacuum dried and derivatized by methoxyamination followed by silylation. Derivatized samples were analyzed by GC-MS. GC-MS analysis was performed on an Agilent 5977A mass spectrometer with a quadrupole analyzer and an HP-5MS UI capillary column (30 m × 0.25 mm × 0.25 mm; Agilent 19091S-433UI). Mass spectra were acquired in electron impact mode (70 eV), with a scan range of 30–650 m/z and a solvent delay of 8 min. Each sample was injected in duplicate as technical replicates. Peak deconvolution, spectral matching, and integration were performed using MassHunter GC/MS Acquisition and MassHunter Qualitative software (Agilent Technologies). C7-C30 alkanes were used for peak alignment. Metabolites were annotated by comparing spectra with the NIST commercial library (Ausloos et al., 1999) and manually validated against the Golm Metabolome Database (GMD; (Kopka, 2006)).
Project description:This series represents the data set described in the publication “Genetic and Immunohistochemical Analysis of Localized Extranodal and Nodal Dendritic Cell Tumours – An Outlook for Individualized Therapies in Rare Tumours” by Ullmann et al. (submitted). Keywords: array CGH