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Implementation of Automated Sample Quality Control in Whole Exome Sequencing

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Journal of Life Sciences 2017年第6期11卷 261-268页

作者： Elisa Viering Jana Molitor Leslie Friedmann Jana Petersen Marie Beckhaus Stephan Wolf Agilent Technologies Inc. Waldbronn 76337 Germany dkfz genomics and proteomics core facility High Throughput Sequencing Unit Heidelberg 69120 Germany

Genetic and Proteomic Analyses of a Xanthomonas campestris *** purC Mutant Deficient in Purine Biosynthesis and Virulence

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Journal of Genetics and genomics 2013年第9期40卷 473-487页

作者： Zhihui Yuan Li Wang Shutao Sun Yao Wu Wei Qian State Key Laboratory of Plant genomics Institute of MicrobiologyChinese Academy of Sciences University of Chinese Academy of Sciences Center of core facility Institute of MicrobiologyChinese Academy of Sciences

Bacterial proliferation in hosts requires activation of a number of housekeeping pathways, including purine de novo biosynthesis. Although inactivation of purine biosynthesis genes can attenuate virulence, it is unclear which biochemical or virulence factors are associated with the purine biosynthesis pathway in vivo. We report that inactivation of purC, a gene encoding phosphoribosylaminoimidazole-succinocarboxamide synthase, caused complete loss of virulence in Xanthomonas campestris pv. cam- pestris, the causal agent of black rot disease of cruciferous plants. The purC mutant was a purine auxotroph; it could not grow on minimal medium, whereas addition of purine derivatives, such as hypoxanthine or adenine plus guanine, restored growth of the mutant. The purC mutation also significantly enhanced the production of an unknown purine synthesis associated pigment and extracellular polysaccharides by the bacterium. In addition, comparative proteomic analyses of bacteria grown on rich and minimal media revealed that the purC mutation affected the expression levels of diverse proteins involved in purine and pyrimidine synthesis, carbon and energy metabolisms, iron uptake, proteolysis, protein secretion, and signal transduction. These results provided clues to understanding the contributions of purine synthesis to bacterial virulence and interactions with host immune systems.

关键词： Purine biosynthesis Virulence Xanthomonas campestris pv. campestris proteomics

MeRIP-PF:An Easy-to-use Pipeline for High-resolution Peak-finding in MeRIP-Seq Data

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genomics, proteomics & Bioinformatics 2013年第1期11卷 72-75页

作者： Yuli Li Shuhui Song Cuiping Li Jun Yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences core Genomic facility Beijing Institute of GenomicsChinese Academy of Sciences

RNA modifications, especially methylation of the N6 position of adenosine （A）--m6A, rep- resent an emerging research frontier in RNA biology. With the rapid development of high-throughput sequencing technology, in-depth study of m6A distribution and function relevance becomes feasible. However, a robust method to effectively identify m6A-modified regions has not been available yet. Here, we present a novel high-efficiency and user-friendly analysis pipeline called MeRIP-PF for the signal identification of MeRIP-Seq data in reference to controls. MeRIP-PF provides a statistical P-value for each identified m6A region based on the difference of read distribution when compared to the con- trols and also calculates false discovery rate （FDR） as a cut offto differentiate reliable m6A regions from the background. Furthermore, MeRIP-PF also achieves gene annotation ofm6A signals or peaks and produce outputs in both XLS and graphical format, which are useful for further study. MeRIP-PF is implemented in Perl and is freely available at http：//***/***.

关键词： RNA modification m 6A Peak finding MeRIP-Seq

A Global Multiregional Proteomic Map of the Human Cerebral Cortex

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genomics, proteomics & Bioinformatics 2022年第4期20卷 614-632页

作者： Zhengguang Guo Chen Shao Yang Zhang Wenying Qiu Wenting Li Weimin Zhu Qian Yang Yin Huang Lili Pan Yuepan Dong Haidan Sun Xiaoping Xiao Wei Sun Chao Ma Liwei Zhang core facility of Instrument Institute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic MedicinePeking Union Medical CollegeBeijing 100005China State Key Laboratory of proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijing 102206China Department of Neurosurgery China National Clinical Research Center for Neurological DiseasesBeijing Tiantan HospitalCapital Medical UniversityBeijing 100050China Department of Human Anatomy Histologyand EmbryologyInstitute of Basic Medical SciencesNeuroscience CenterChinese Academy of Medical SciencesSchool of Basic MedicinePeking Union Medical CollegeBeijing 100005China

The Brodmann area(BA)-based map is one of the most widely used cortical maps for studies of human brain functions and in clinical practice;however,the molecular architecture of BAs remains *** present study provided a global multiregional proteomic map of the human cerebral cortex by analyzing 29 *** 29 BAs were grouped into 6 clusters based on similarities in proteomic patterns:the motor and sensory cluster,vision cluster,auditory and Broca’s area cluster,Wernicke’s area cluster,cingulate cortex cluster,and heterogeneous function *** identified 474 cluster-specific and 134 BA-specific signature proteins whose functions are closely associated with specialized functions and disease vulnerability of the corresponding cluster or *** findings of the present study could provide explanations for the functional connections between the anterior cingulate cortex and sensorimotor cortex and for anxiety-related function in the sensorimotor *** brain transcriptome and proteome comparison indicates that they both could reflect the function of cerebral cortex,but show different *** proteomic data are publicly available at the Human Brain Proteome Atlas(***).Our results may enhance our understanding of the molecular basis of brain functions and provide an important resource to support human brain research.

关键词： Brodmann area proteomics Cerebral cortex Cingulate cortex Sensorimotor cortex

Developing Novel Protein Biomarker Assays for Early Diagnosis of Pancreatic Cancer

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Developing Novel Protein Biomarker Assays for Early Diagnosi...

Single-cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-genesis in Pigs

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作者： Raghavakaimal Sreekumar Associate Professor Department of Endocrinology DirectorGCRC GenomicsProteomics and Metabolic Core Facility ＆ Mayo Genomic Center Microarray LaboratoryMayo ClinicRochesterMNUSA.

＜正＞Glucose intolerance occurs in up to 80% of pancreatic cancer （PaC） patients. There is evidence to suggest that diabetes induced by PaC （PaCDM） is a paraneoplastic phenomenon caused by as yet unknown humoral mediators . The aim of this study is to identify, from serum and PaC tissue, biomarkers unique to PaC, quantify the potential markers and develop assays to screen the patients at risk for PaC. Carefully and extensively annotated samples from thousands of patients with a variety of disease and from healthy controls have already been and continue to be prespectively collected at Mayo Clinic under the auspices of the Pancreas Cancer SPORE Biospecimen repositories. These sera will be used for a thorough and comprehensive evaluation of the sensitivity and specificity of identified biomarkers. This proposal will complete Phases 1 and 2 of Biomarker Development adopted by the NCI’ s Early Detection Research Network . We use the iTRAQ protocol which allows for relative and absolute quantitation of proteins in up to 4 samples in a single LC - MS/MS analysis and we have identified several promising serum biomarker in our preliminary studies from tissue as well as serum. For tissue proteomics we used laser capture microdissection （LCM） to get a population of pure pancreatic cancer cells from PaC tissue. Analytical Validation of Biomarkers discovered from serum and tissue is completed . We are currently trying to determine their sensitivity and specificity to distinguish PaC and PaCDM from type 2 DM, other cancers and healthy controls. Identification of specific biomarkers（s） for PaCDM will allow targeting of select individuals with elevated fasting blood glucose for more intensive screening for PaC.

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genomics, proteomics & Bioinformatics 2021年第3期19卷 423-436页

作者： Jianbo Li Ligang Wang Dawei Yu Junfeng Hao Longchao Zhang Adeniyi C.Adeola Bingyu Mao Yun Gao Shifang Wu Chunling Zhu Yongqing Zhang Jilong Ren Changgai Mu David M.Irwin Lixian Wang Tang Hai Haibing Xie Yaping Zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China core facility for Protein Research Institute of BiophysicsChinese Academy of SciencesBeijing 100101China State Key Laboratory for Molecular and Developmental Biology CAS Center for Excellence in Brain Science and Intelligence TechnologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650223China Department of Laboratory Medicine and Pathobiology University of TorontoTorontoOntario M5S1A8Canada Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Development of thoracolumbar vertebra(TLV)and rib primordium(RP)is a common evolutionary feature across vertebrates,although whole-organism analysis of the expression dynamics of TLV-and RP-related genes has been ***,we investigated the single-cell transcriptome landscape of thoracic vertebra(TV),lumbar vertebra(LV),and RP cells from a pig embryo at 27 days post-fertilization(dpf)and identified six cell types with distinct gene expression ***-depth dissection of the gene expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and RP *** analysis of cell type-specific and strand-specific expression uncovered the extremely high level of HOXA103′-UTR sequence specific to osteoblasts of LV cells,which may function as anti-HOXA10-antisense by counteracting the HOXA10-antisense effect to determine TLV ***,this work provides a valuable resource for understanding embryonic osteogenesis and angiogenesis underlying vertebrate TLV and RP development at the cell type-specific resolution,which serves as a comprehensive view on the transcriptional profile of animal embryo development.

关键词： scRNA-seq Thoracolumbar vertebra transition Rib-genesis Osteogenesis Angiogenesis