Project description:Classification of a large micro-array dataset. Algorithm comparison and analysis of drug signatures. These data support the publication titled "Classification of a large micro-array dataset. Algorithm comparison and analysis of drug signatures.". Some of the calculations in the publication were derived from an older version of the data available at http://www.iconixpharm.com Copyright (c) 2005 by Iconix Pharmaceuticals, Inc. Guidelines for commercial use: http://www.iconixbiosciences.com/guidelineCommUse.pdf Keywords: other
Project description:Raptor expression was specifically deleted in the tubular system of the kidney using an inducible Cre-Lox system under the control of a Pax8 promotor. Please see further details concerning the experimental procedures in the accompanied publication
Project description:We have created a resource of single cell transcriptome data from the model organism Mus musculus. Contributor: The Tabula Muris Consortium The full list of contributors to this dataset can be found in the corresponding publication.
Project description:Early multiple sclerosis lesions feature relative preservation of oligodendrocyte cell bodies with dying back retraction of their myelinating processes. Cell loss occurs with disease progression. Putative injury mediators include metabolic stress (low glucose/nutrient), pro-inflammatory mediators (interferon γ and tumor necrosis factor a), and excitotoxins (glutamate). Our objective was to compare the impact of these disease relevant mediators on the injury responses of human mature oligodendrocytes. In the current study, we determined the effects of these mediators on process extension and survival of human brain derived mature oligodendrocytes in vitro and used bulk RNA sequencing to identify distinct effector mechanisms that underlie the responses. All mediators induced significant process retraction of the oligodendrocytes in dissociated cell culture. Only metabolic stress (low glucose/nutrient) conditions resulted in delayed (4-6 days) non-apoptotic cell death. Metabolic effects were associated with induction of the integrated stress response, which can be protective or contribute to cell injury dependent on its level and duration of activation. Addition of Sephin1, an agonist of the integrated stress response induced process retraction under control conditions and further enhanced retraction under metabolic stress conditions. The antagonist ISRIB restored process outgrowth under stress conditions, and if added to already stressed cells, reduced delayed cell death and prolonged the period in which recovery could occur. Inflammatory cytokine functional effects were associated with activation of multiple signaling pathways (including Jak/Stat-1) that regulate process outgrowth, without integrated stress response induction. Glutamate application produced limited transcriptional changes suggesting a contribution of effects directly on cell processes.
Project description:Parental and 5-fluorouracil (5-FU)-resistant HCT15 cells were treated with 5-FU or vehicle for 12h and assembled into an IMPRINTS-CETSA scheme with 6 different heating temperatures (37ºC, 47ºC, 50ºC, 52ºC, 54ºC, and 57ºC) with each set of samples heated at one temperature included in the same isobaric TMT10 set and measured at the same time on the mass spectrometer.
This entry contains two datasets:
1. 5-FU in parental vs. resistant HCT15 (file names “12h 5FU_par vs resHCT15”) for data referred to as HCT15_Par_5FU and HCT15_Res_5FU in the associated publication. The labelling order of samples in the TMT10 channels for this dataset was as follows: 37C/47C/50C/52C/54C/57C samples: Biorep1_Parental_Vehicle (126), Biorep1_Parental_5FU_100µM (127N), Biorep1_Resistant_5FU_16µM (127C), Biorep2_ Parental_Vehicle (128N), Biorep2_ Parental_5FU_100µM (128C), Biorep2_ Resistant_5FU_16µM (129N), Biorep3_ Parental_Vehicle (129C), Biorep3_ Parental_5FU_100µM (130N), Biorep3_ Resistant_5FU_16µM (130C), mixed_control (131).
2. 5-FU in resistant HCT15 (file names “12h 5FU_ResHCT15_diff”) for data referred to as HCT15_Res_Diff in the in the associated publication. The labelling order of samples in the TMT10 channels for this dataset was as follows: 37C/47C/50C/52C/54C/57C samples: Biorep1_ Resistant_5FU_16µM (128N), Biorep2_ Resistant_5FU_16µM (128C), Biorep3_ Resistant_5FU_16µM (129N), Biorep1_ Resistant_5FU_100µM (129C), Biorep2_ Resistant_5FU_100µM (130N), Biorep3_ Resistant_5FU_100µM (130C), mixed_control (131).
For additional details see the methods section of the associated publication.
Project description:This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/In this study we aim to assess the 5-formylcytosine profile in tissues from control and Thymine DNA Glycosylase (TDG)-deleted embryos by pulling down and sequencing 5fC-containing DNA (method from Raiber et al., 2012).
Project description:To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium.These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Project description:Classification of a large micro-array dataset. Algorithm comparison and analysis of drug signatures. These data support the publication titled "Classification of a large micro-array dataset. Algorithm comparison and analysis of drug signatures.". Some of the calculations in the publication were derived from an older version of the data available at http://www.iconixpharm.com Copyright (c) 2005 by Iconix Pharmaceuticals, Inc. Guidelines for commercial use: http://www.iconixbiosciences.com/guidelineCommUse.pdf
