Project description:The Chromosome 16 Consortium is integrated in the Human Proteome Project that aims to develop an entire map of the proteins encoded by the human genome following a gene-centric strategy (C-HPP) to make progress in the understanding of human biology in health and disease (B/D-HPP). To do this study four human cell lines were selected, MCF7 epithelial cells, CCD18 colon fibroblasts, Ramos and Jurkat B and T lymphocytes respectively. In particular, this subset includes all the data regarding the CCD18 cell line. 6 laboratories contributed to compile all the reported data.
Project description:To understand whether hematopoietic stem cells (HSCs) take part in emergency granulopoiesis, WT C57BL6 mice were treated intraperitoneally with 35 ug of lipopolysacharide (LPS) to induce emergency granulopoiesis, or PBS control. Mice were sacrificed 4 hours after the treatment and HSCs (Lin-c-Kit+Sca-1+CD48-CD150+) were sorted and subjected to bulk ATACseq.
Project description:To uncover the chromosome 16 associated proteome and to take advantage of the generated knowledge to make progress in human biology in health and disease, a consortium of 15 groups was organized in four working groups: SRM and protein sequencing, antibody and peptide standard, clinical healthcare and biobanking and bioinformatics. According to a preliminary in silico study integrating knowledge from Ensembl, UniProt and GPM, Ramos B lymphocyte cells, MCF-7 epitelial cells and CCD18 fibroblast were selected as it is theoretically expected that any chromosome 16 protein coding gene is expressed in at least one of them. To define in detail the transcriptome of the above mentioned cell lines Affymetrix microarray based analyses were performed. Upon hybridization in Human ST 1.0 arrays, raw data were processed with RMA algorithm for background correction and normalization. Chromosome 16 gene expression pattern was then defined in each cell line and comparative analysis was done with R package statistics. Biological functions involving chromosome 16 genes were analysed with GO and functional networks were studied with Ingenuity Pathway Analysis. Expressed genes were compared with data from shotgun proteomic experiments to find the degree of correlation mRNA-protein. Expression of genes coding for proteins with weak or none MS evidence is shown. The integration of this information in decision-making process of the mass spectrometry group is discussed. Expression profiles of MCF7, CCD18 and Ramos human cell lines.
