Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils
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C. Tuggle | M. Schroyen | J. Koltes | Haibo Liu | C. Loving | Kristen A. Byrne | J. Herrera-Uribe | K. Lim | Lance Daharsh | R. Corbett | Gianna Marco
[1] C. Ernst,et al. Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits , 2022, BMC Genomics.
[2] P. VanRaden,et al. A multi-tissue atlas of regulatory variants in cattle , 2022, Nature Genetics.
[3] S. Gregory,et al. Single Cell RNA-Seq Analysis of Human Red Cells , 2022, Frontiers in Physiology.
[4] M. Lund,et al. Pig genome functional annotation enhances the biological interpretation of complex traits and human disease , 2021, Nature Communications.
[5] A. Moore,et al. DNA methylation signatures reveal that distinct combinations of transcription factors specify human immune cell epigenetic identity. , 2021, Immunity.
[6] Steven B. Cogill,et al. Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection , 2021, Life Science Alliance.
[7] B. Walzog,et al. Distinct transcription factor networks control neutrophil-driven inflammation , 2021, Nature Immunology.
[8] U. Demkow,et al. Phagocytosis, Degranulation and Extracellular Traps Release by Neutrophils—The Current Knowledge, Pharmacological Modulation and Future Prospects , 2021, Frontiers in Pharmacology.
[9] B. O’Malley,et al. Mechanisms of enhancer action: the known and the unknown , 2021, Genome biology.
[10] J. Lunney,et al. Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing , 2021, bioRxiv.
[11] Alison L. Van Eenennaam,et al. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research , 2021, Nature Communications.
[12] J. Dekkers,et al. Gene expression in tonsils in swine following infection with porcine reproductive and respiratory syndrome virus , 2021, BMC Veterinary Research.
[13] Qianying Zhang,et al. Neutrophil-to-lymphocyte ratio correlates with prognosis and response to chemotherapy in patients with non-M3 de novo acute myeloid leukemia , 2021, Translational cancer research.
[14] F. Du,et al. MXD1 is a Potential Prognostic Biomarker and Correlated With Specific Molecular Change and Tumor Microenvironment Feature in Esophageal Squamous Cell Carcinoma , 2021, Technology in cancer research & treatment.
[15] D. Hume,et al. Network analysis of transcriptomic diversity amongst resident tissue macrophages and dendritic cells in the mouse mononuclear phagocyte system , 2020, PLoS biology.
[16] S. Mostafavi,et al. Deep learning of immune cell differentiation , 2020, Proceedings of the National Academy of Sciences.
[17] C. Tuggle,et al. Differential induction of innate memory in porcine monocytes by β-glucan or bacillus Calmette-Guerin , 2020, Innate immunity.
[18] Min Yang,et al. Salmonella enterica serovar Typhimurium inhibits the innate immune response and promotes apoptosis in a ribosomal/TRP53-dependent manner in swine neutrophils , 2020, Veterinary Research.
[19] C. Tuggle,et al. Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure , 2020, Frontiers in Genetics.
[20] F. Ginhoux,et al. Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor. , 2020, Immunity.
[21] T. Cheng,et al. Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection , 2020, Nature Immunology.
[22] N. de Buhr,et al. What Is the Evolutionary Fingerprint in Neutrophil Granulocytes? , 2020, International journal of molecular sciences.
[23] J. Rioux,et al. A transcriptome-based approach to identify functional modules within and across primary human immune cells , 2020, PloS one.
[24] P. Proost,et al. Truncation of CXCL8 to CXCL8(9‐77) enhances actin polymerization and in vivo migration of neutrophils , 2020, Journal of leukocyte biology.
[25] P. Proost,et al. Neutrophil chemoattractant receptors in health and disease: double-edged swords , 2020, Cellular & Molecular Immunology.
[26] J. Cyster,et al. The transcription factor Hhex cooperates with the corepressor Tle3 to promote memory B cell development , 2020, bioRxiv.
[27] Philip A. Ewels,et al. The nf-core framework for community-curated bioinformatics pipelines , 2020, Nature Biotechnology.
[28] Feng Yan,et al. From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis , 2020, Genome Biology.
[29] V. Nizet,et al. Upon microbial challenge, human neutrophils undergo rapid changes in nuclear architecture and chromatin folding to orchestrate an immediate inflammatory gene program , 2020, Genes & development.
[30] Hong-Wei Sun,et al. Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus , 2019, Proceedings of the National Academy of Sciences.
[31] Michal R. Grzadkowski,et al. Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia , 2019, Nature Communications.
[32] J. Ritchey,et al. Neutrophils Induce a Novel Chemokine Receptors Repertoire During Influenza Pneumonia , 2019, Front. Cell. Infect. Microbiol..
[33] Alireza Hadj Khodabakhshi,et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets , 2019, Nature Communications.
[34] G. Lenz,et al. Safeguard function of PU.1 shapes the inflammatory epigenome of neutrophils , 2019, Nature Immunology.
[35] K. Qu,et al. Landscape and Dynamics of the Transcriptional Regulatory Network During Natural Killer Cell Differentiation , 2019, bioRxiv.
[36] C. Tuggle,et al. Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. , 2019, Annual review of animal biosciences.
[37] M. Ceccarelli,et al. RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types , 2019, Cell reports.
[38] P. Qiu,et al. Correlation Patterns Between DNA Methylation and Gene Expression in The Cancer Genome Atlas , 2019, Cancer informatics.
[39] Damian Szklarczyk,et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..
[40] Wei Shi,et al. Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans , 2018, Nucleic Acids Res..
[41] I. Adcock,et al. Update on Neutrophil Function in Severe Inflammation , 2018, Front. Immunol..
[42] A. Valencia,et al. Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils , 2018, Cell reports.
[43] A. M. Guimarães,et al. RNA-Seq based transcriptome of whole blood from immunocompetent pigs (Sus scrofa) experimentally infected with Mycoplasma suis strain Illinois , 2018, Veterinary Research.
[44] S. Mundlos,et al. Loss of murine Gfi1 causes neutropenia and induces osteoporosis depending on the pathogen load and systemic inflammation , 2018, PloS one.
[45] B. Kerr,et al. Influence of feeding thermally peroxidized soybean oil on oxidative status in growing pigs. , 2018, Journal of animal science.
[46] Deepak Kumar Jha,et al. Reconstruction of complex single-cell trajectories using CellRouter , 2018, Nature Communications.
[47] Jun Yu,et al. ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data , 2018, BMC Genomics.
[48] C. Rosales. Neutrophil: A Cell with Many Roles in Inflammation or Several Cell Types? , 2018, Front. Physiol..
[49] Brandon J Thomas,et al. IL-10 Signaling Remodels Adipose Chromatin Architecture to Limit Thermogenesis and Energy Expenditure , 2018, Cell.
[50] C. Hong. Current Understanding in Neutrophil Differentiation and Heterogeneity , 2017, Immune network.
[51] Shuhong Zhao,et al. Transcriptomic basis of neutrophil ratio variation induced by poly I:C stimulation in porcine peripheral blood , 2017 .
[52] Yen Ching Lim,et al. A complex association between DNA methylation and gene expression in human placenta at first and third trimesters , 2017, PloS one.
[53] Jason D. Buenrostro,et al. Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans , 2017, bioRxiv.
[54] J. Dekkers,et al. A high-quality annotated transcriptome of swine peripheral blood , 2017, BMC Genomics.
[55] Hongjun Chen,et al. Non-coding Transcripts from Enhancers: New Insights into Enhancer Activity and Gene Expression Regulation , 2017, Genom. Proteom. Bioinform..
[56] I. Amit,et al. Genomic Characterization of Murine Monocytes Reveals C/EBP&bgr; Transcription Factor Dependence of Ly6C− Cells , 2017, Immunity.
[57] E. Anguita,et al. Transcription Factor GFI1B in Health and Disease , 2017, Front. Oncol..
[58] Geet Duggal,et al. Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.
[59] J. Corbo,et al. Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors , 2017, Scientific Reports.
[60] G. Ming,et al. Neuronal activity modifies the chromatin accessibility landscape in the adult brain , 2017, Nature Neuroscience.
[61] João Pedro de Magalhães,et al. Gene co-expression analysis for functional classification and gene–disease predictions , 2017, Briefings Bioinform..
[62] Julio Saez-Rodriguez,et al. OmniPath: guidelines and gateway for literature-curated signaling pathway resources , 2016, Nature Methods.
[63] John Quackenbush,et al. Smooth Quantile Normalization , 2016, bioRxiv.
[64] Alfonso Valencia,et al. Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types , 2016, bioRxiv.
[65] John Quackenbush,et al. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data , 2016, BMC Bioinformatics.
[66] Howard Y. Chang,et al. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing , 2016, Nature Methods.
[67] Anna L. Brown,et al. Conditional knockout mice demonstrate function of Klf5 as a myeloid transcription factor. , 2016, Blood.
[68] Måns Magnusson,et al. MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..
[69] Anna Huttenlocher,et al. Neutrophil migration in infection and wound repair: going forward in reverse , 2016, Nature Reviews Immunology.
[70] E. Fraenkel,et al. Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells , 2016, Scientific Reports.
[71] Fidel Ramírez,et al. deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..
[72] J. Schug,et al. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes , 2016, Molecular metabolism.
[73] T. Kaisho,et al. PDLIM1 inhibits NF-κB-mediated inflammatory signaling by sequestering the p65 subunit of NF-κB in the cytoplasm , 2015, Scientific Reports.
[74] Rafael A. Irizarry,et al. quantro: a data-driven approach to guide the choice of an appropriate normalization method , 2015, Genome Biology.
[75] Howard Y. Chang,et al. ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide , 2015, Current protocols in molecular biology.
[76] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[77] Fidel Ramírez,et al. deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..
[78] M. Bahlo,et al. GFI1B mutation causes a bleeding disorder with abnormal platelet function , 2013, Journal of Thrombosis and Haemostasis.
[79] Howard Y. Chang,et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.
[80] Kent Milfeld,et al. Optimizing the PCIT algorithm on stampede's Xeon and Xeon Phi processors for faster discovery of biological networks , 2013, XSEDE.
[81] Nathan C. Sheffield,et al. The accessible chromatin landscape of the human genome , 2012, Nature.
[82] Nathan C. Sheffield,et al. Predicting cell-type–specific gene expression from regions of open chromatin , 2012, Genome research.
[83] Shizuo Akira,et al. Matrix Metalloprotease 9 Mediates Neutrophil Migration into the Airways in Response to Influenza Virus-Induced Toll-Like Receptor Signaling , 2012, PLoS pathogens.
[84] V. Ranieri,et al. The RacGAP ArhGAP15 is a master negative regulator of neutrophil functions. , 2011, Blood.
[85] M. Tschan,et al. Deregulated expression of Kruppel-like factors in acute myeloid leukemia. , 2011, Leukemia research.
[86] J. Garrido,et al. Gene expression pattern in swine neutrophils after lipopolysaccharide exposure: a time course comparison , 2011, BMC proceedings.
[87] J. Jansen,et al. Gfi1 and Gfi1b: key regulators of hematopoiesis , 2010, Leukemia.
[88] Aaron R. Quinlan,et al. Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .
[89] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[90] E. Birney,et al. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.
[91] M. Colonna,et al. Activation of an Immunoregulatory and Antiviral Gene Expression Program in Poly(I:C)-Transfected Human Neutrophils1 , 2008, The Journal of Immunology.
[92] Antonio Reverter,et al. Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks , 2008, Bioinform..
[93] T. Möröy,et al. Gfi1b:green fluorescent protein knock-in mice reveal a dynamic expression pattern of Gfi1b during hematopoiesis that is largely complementary to Gfi1. , 2007, Blood.
[94] Daniel G. Tenen,et al. Transcription factors in myeloid development: balancing differentiation with transformation , 2007, Nature Reviews Immunology.
[95] L. Luzzatto,et al. CD157 plays a pivotal role in neutrophil transendothelial migration. , 2006, Blood.
[96] B. Heit,et al. HIV and Other Lentiviral Infections Cause Defects in Neutrophil Chemotaxis, Recruitment, and Cell Structure: Immunorestorative Effects of Granulocyte-Macrophage Colony-Stimulating Factor1 , 2006, The Journal of Immunology.
[97] M. Pipkin,et al. A reliable method to display authentic DNase I hypersensitive sites at long-ranges in single-copy genes from large genomes , 2006, Nucleic acids research.
[98] Mike Tyers,et al. BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..
[99] T. Möröy,et al. Direct transcriptional repression of the genes encoding the zinc-finger proteins Gfi1b and Gfi1 by Gfi1b , 2005, Nucleic acids research.
[100] L. Luzzatto,et al. CD157 is an important mediator of neutrophil adhesion and migration. , 2004, Blood.
[101] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[102] Z. Duan,et al. Gfi-1 Oncoproteins in Hematopoiesis , 2003, Hematology.
[103] J. Cowland,et al. The in vivo profile of transcription factors during neutrophil differentiation in human bone marrow. , 2003, Blood.
[104] Gary D. Bader,et al. An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.
[105] S. Cameron,et al. The zinc-finger proto-oncogene Gfi-1b is essential for development of the erythroid and megakaryocytic lineages. , 2002, Genes & development.
[106] Thomas D. Schmittgen,et al. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.
[107] E. Querfurth,et al. GATA-1 interacts with the myeloid PU.1 transcription factor and represses PU.1-dependent transcription. , 2000, Blood.
[108] M. Arnone,et al. Using ATAC-seq and RNA-seq to increase resolution in GRN connectivity. , 2019, Methods in cell biology.
[109] S. Brunak,et al. A scored human protein–protein interaction network to catalyze genomic interpretation , 2017, Nature Methods.
[110] S. Corey,et al. Systems approach to phagocyte production and activation: neutrophils and monocytes. , 2014, Advances in experimental medicine and biology.
[111] S. K. Zaidi,et al. Transcription factor-mediated epigenetic regulation of cell growth and phenotype for biological control and cancer. , 2010, Advances in enzyme regulation.
[112] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .