Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a pilot submission of mass-spectrometry analyses from 18 induced pluripotent stem cell lines generated by the HipSci project. This submission includes also data for two embryonic stem cell lines, and one reference sample comprising a mixture of 42 IPSC lines. Raw data files for this study can be accessed from the PRIDE database at EMBL-EBI under accession number PXD003903: http://www.ebi.ac.uk/pride/archive/projects/PXD003903.
Project description:Chronic kidney disease remains an unmet clinical challenge. It is only detected at advanced stages by current markers. Therefore, early detection of chronic kidney disease is vital. In this study, we profiled the urinary proteome in patients with albuminuria with well-preserved eGFR. We identi-fied 80 proteins that were differentially abundant between cases (albuminuria) and controls (normoalbuminuria). Among these, 12 proteins (SERPINA1, ALB, SERPINC1, AFM, PIGR, A1BG, COL6A1, MYG, LV39, MUC1, ICOSLG, and UMOD) had the highest discriminating abilities (area under curve > 0.8) between cases and controls. When differentially abundant proteins were com-bined into an 80-protein model, the model was able to predict cases from controls with predictive accuracy of 91.3%. The top five enriched biological pathways associated with differentially abundant proteins included insulin growth factor functions, innate immunity, platelet degranula-tion, and extracellular matrix organization.
Project description:Both SKOV3 and IOSE80 cells were cultured and extracted the proteins. With sequential digestion by trypsin, enriched by Zwitterionic Hydrophilic Interaction chromatography (ZIC-HILIC), the intact N-glycopeptides were then isotopic diethyl labelled and analyzed using C18-RPLC-MS/MS (HCD).
Project description:To establish a systematic approach for the determination of human biological & disease relevance through the generation of epigenome data in cell types of interest. Integration of cell type epigenome data with existing & newly generated reference data from human tissue and cell types to identify assay systems which will provide greater confidence in translating target biology and compound pharmacology to patients. To provide a framework for the identification of optimal cell types for target identification/validation studies and drug discovery programs across multiple therapeutic areas. Development of bioinformatics pipelines and CTTV components for analysis and provision of data
Project description:These RNAseq experiments are carried out as part of the CTTV020 project to identify a gene expression signature of common immortalised cell lines / models. This signature / fingerprint will be used in combination with data from ChIPseq experiments from the same cell types to compare various human immortalised cell models against primary cells and tissues. The overall aims of the CTTV020 Cell Line Epigenome project are to establish a systematic approach for the determination of human biological & disease relevance through the generation of transciptomic and epigenomic data in cell types of interest \Integration of cell type mRNA expression and epigenome data with existing & newly generated reference data from human tissue and cell types to identify assay systems which will provide greater confidence in translating target biology and compound pharmacology to patients.\To provide a framework for the identification of optimal cell types for target identification/validation studies and drug discovery programs across multiple therapeutic areas. \Development of bioinformatics pipelines and CTTV components for analysis and provision of dataThis 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/
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a pilot submission of mass-spectrometry analyses from 18 induced pluripotent stem cell lines generated by the HipSci project. This submission includes also data for two embryonic stem cell lines, and one reference sample comprising a mixture of 42 IPSC lines. Associated BioSamples accessions: <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2397999">SAMEA2397999</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398167">SAMEA2398167</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398916">SAMEA2398916</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2397948"> SAMEA2397948 </a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2399112">SAMEA2399112</a>,<a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2399257">SAMEA2399257</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398553">SAMEA2398553</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398821">SAMEA2398821</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398316">SAMEA2398316</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2469778">SAMEA2469778</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2399037">SAMEA2399037</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398656">SAMEA2398656</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398428">SAMEA2398428</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2469777">SAMEA2469777</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2397959">SAMEA2397959</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398442">SAMEA2398442</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398024">SAMEA2398024</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398450">SAMEA2398450</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA3402864">SAMEA3402864</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA3110364">SAMEA3110364</a>
Project description:Galectin-7 expression was found to be strongly reduced in cervical cancer cell lines. The same tumor cell lines in which Galectin-7 was ectopically expressed exhibited significant decrease in their tumorigenic capacity in vitro and in vivo. The proteomic changes in the cervical cancer cell lines HeLa and SiHa after Galectin-7 re-expression were here quantified by SILAC.