Project description:The Russian part of C-HPP is aimed to identify proteins encoded by the 18 human chromosome. In this project, 3 liver tissue samples were studied by standart Shotgun and 2 dimensional liquid chromatography approach to enhance the sensitivity of the MS method. The total amount of proteins found in samples is 5022 and the proteins encoded by the 18 human chromosome is 64.
Project description:The Russian part of C-HPP is aimed to identify proteins encoded by the 18 human chromosome. In this project, 3 liver tissue samples were studied by standart SRM and 2 dimensional liquid chromatography approach to enhance the sensitivity of the MS method. The total amount of proteins found in samples encoded by the 18 human chromosome is 118. UPS1 used as calibration and to measure the sensitivity of SRM method.
Project description:We report that inhibition of rho by treatment with bicyclomycin, a potential inhibitor of rho affects H-NS binding to chromosome across most of the binding sites. For the current study, we have flag tagged H-NS by homologous recomination method. Cells were grown in the presence and absence of antibiotic bicylomyin. Chromatin immunoprecipitation was performed and anti flag antibody was used for immunoprecipitation. Immunoprecipitated samples both from BCM- and BCM + conditions were sequenced using HiSeq 1000 model. Input DNA was used as control for this experiment which was also sequenced. The 50-mer reads obtained were then mapped to Escherichia coli Mg1655 K-12 genome. Further analysis was carried out to calculate the ChIP signal score. We observed a drop in ChIP signal for bcm+ condition as compared to bcm-. ChIP-seq data generated by Hiseq 1000 model of samples with bcm+ and bcm- in biological duplicates along with Input DNA as control
Project description:We report that inhibition of rho by treatment with bicyclomycin, a potential inhibitor of rho affects H-NS binding to chromosome across most of the binding sites. For the current study, we have flag tagged H-NS by homologous recomination method. Cells were grown in the presence and absence of antibiotic bicylomyin. Chromatin immunoprecipitation was performed and anti flag antibody was used for immunoprecipitation. Immunoprecipitated samples both from BCM- and BCM + conditions were sequenced using HiSeq 1000 model. Input DNA was used as control for this experiment which was also sequenced. The 50-mer reads obtained were then mapped to Escherichia coli Mg1655 K-12 genome. Further analysis was carried out to calculate the ChIP signal score. We observed a drop in ChIP signal for bcm+ condition as compared to bcm-.
Project description:In the boundaries of chromosome-centric Human Proteome Project c-HPP to obtain information about proteoforms coded by chromosome 18, several cell lines were analyzed. In our study we have been using proteoform separation by 2DE (sectional analysis) and semi-virtual 2DE with following shotgun mass-spectrometry using LC ESI-MS/MS. Previously, we published a first draft of this research, where only HepG2 cells were used. Here, next step was done using liver, glioblastoma, fibroblasts, kidney cells and plasma. Altogether, confident (2 significant sequences minimum) information about proteoforms coded by ~80 genes was obtained. The 3D-graphs showing distribution of different proteoforms from the same gene in 2D map were generated. Additionally, semi-virtual 2DE approach allowed for detecting more proteoforms and estimate their pI more precisely
Project description:For the analysis of chromosome 11-centric human proteome, we analyzed the human brain hippocampal proteome. The samples from brain tissues were extensively off-gel fractionated by 12 fractions and analyzed by a high resolution mass spectrometer, Orbitrap XL ETD with collision induced dissociation, after LC separation using C18 column.
Project description:This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
Project description:This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
