Searching across hundreds of databases
Upon activation, naive CD4+ T cells differentiate into distinct T cell subsets via processes reliant on epigenetically regulated, lineage-specific developmental programs. Here, we examined the function of the histone methyltransferase SETDB1 in T helper (Th) cell differentiation. Setdb1-/- naive CD4+ T cells exhibited exacerbated Th1 priming, and when exposed to a Th1-instructive signal, Setdb1-/- Th2 cells crossed lineage boundaries and acquired a Th1 phenotype. SETDB1 did not directly control Th1 gene promoter activity but relied instead on deposition of the repressive H3K9me3 mark at a restricted and cell-type-specific set of endogenous retroviruses (ERVs) located in the vicinity of genes involved in immune processes. Refined bioinformatic analyses suggest that these retrotransposons regulate Th1 gene cis-regulatory elements or act as Th1 gene enhancers. Thus, H3K9me3 deposition by SETDB1 ensures Th cell lineage integrity by repressing a repertoire of ERVs that have been exapted into cis-regulatory modules to shape and control the Th1 gene network.
Pubmed ID: 30737147 RIS Download
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
View all literature mentionsComputable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
View all literature mentionsOpen, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases.
View all literature mentionsInterferome is a database that provides identification of interferon regulated gene signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It will also assist in identifying regulatory elements and enable comparison of tissue expression of IRGs in human and mouse. Availability of sequence information from more than 37 species, together with comprehensive annotation will enable comparative genomics and phylogenetic analysis to be performed on these IRGs. Within the database, Type I, II and III IFN regulated genes have been manually curated from more than 28 publicly available microarray datasets. Interferon Regulated Genes (IRGs) were identified from multiple microarray and proteomic experiments where cells were treated with IFNs. Genes that were up or down regulated more than 1.5 fold relative to control samples were defined as IRGs.
View all literature mentionsSoftware for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.
View all literature mentionsA generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms.
View all literature mentionsPortal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.
View all literature mentionsSoftware tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.
View all literature mentionsConsortium to coordinate epigenome mapping and characterization worldwide to avoid redundant research effort, to implement high data quality standards, to coordinate data storage, management and analysis and to provide free access to the high resolution reference human epigenome maps for normal and disease cell types to the research community. Promotes data sharing. You may view, search and download the data already released by the different IHEC associated projects via the IHEC Data Portal.
View all literature mentionsPortal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.
View all literature mentionsThis monoclonal targets Siglec-F
View all literature mentionsThis monoclonal targets CD11b
View all literature mentionsThis monoclonal targets CD335 (NKp46)
View all literature mentionsThis polyclonal targets H3K4me1
View all literature mentionsThis polyclonal targets H3K27ac
View all literature mentionsThis polyclonal targets H3K9me3
View all literature mentionsThis monoclonal secondary targets IgG - H&L
View all literature mentionsThis polyclonal targets RCJMB04_4h19
View all literature mentionsThis polyclonal targets Rabbit Rabbit IgG secondary - H&L
View all literature mentionsThis monoclonal targets IFN gamma
View all literature mentionsThis monoclonal targets IL-13
View all literature mentionsThis monoclonal targets IFN gamma
View all literature mentionsThis monoclonal targets KMT1E / SETDB1 antibody [5H6A12]
View all literature mentionsThis monoclonal targets T-bet
View all literature mentionsThis monoclonal targets CD69
View all literature mentionsThis monoclonal targets CD62L (L-Selectin)
View all literature mentionsThis monoclonal targets TNF alpha
View all literature mentionsThis monoclonal targets Gata-3
View all literature mentionsThis monoclonal targets Ly-6G/Ly-6C
View all literature mentionsThis monoclonal targets CD49b (Integrin alpha 2)
View all literature mentionsThis monoclonal targets CD11c
View all literature mentionsThis monoclonal targets CD45R (B220)
View all literature mentionsThis monoclonal targets CD44
View all literature mentionsThis monoclonal targets CD8a
View all literature mentionsThis monoclonal targets MHC Class II (I-A/I-E)
View all literature mentionsThis monoclonal targets CD8a
View all literature mentionsThis monoclonal targets CD317 (BST2, PDCA-1)
View all literature mentionsThis monoclonal targets MHC Class II (I-A/I-E)
View all literature mentionsThis monoclonal targets CD8a
View all literature mentionsThis monoclonal targets CD4
View all literature mentionsThis monoclonal targets CD8b
View all literature mentionsThis monoclonal targets CD8a
View all literature mentionsThis monoclonal targets CD8a
View all literature mentionsThis monoclonal targets H-2Kd
View all literature mentionsThis monoclonal targets Stat4 (pY693)
View all literature mentionsThis monoclonal targets CD69
View all literature mentionsThis unknown targets Ki-67
View all literature mentionsThis monoclonal targets CD11b (Mac-1)
View all literature mentionsThis monoclonal targets CD25 (IL-2 Receptor α)
View all literature mentionsThis monoclonal targets TCR b chain
View all literature mentionsThis monoclonal targets CD4
View all literature mentionsThis monoclonal targets TCR β Chain
View all literature mentionsThis monoclonal targets TCR b chain
View all literature mentionsThis monoclonal targets CD25
View all literature mentionsThis monoclonal targets Mouse CD44
View all literature mentionsThis monoclonal targets CD62L (L-Selectin)
View all literature mentionsThis monoclonal targets IL-4
View all literature mentionsThis monoclonal targets GM-CSF
View all literature mentionsThis monoclonal targets CD3ε
View all literature mentionsThis monoclonal targets IL-4
View all literature mentionsThis monoclonal targets CD28
View all literature mentionsThis monoclonal targets IFNγ
View all literature mentionsAllele Detail: Targeted This is a legacy resource.
View all literature mentionsMus musculus with name B6Dnk;B6N-Setdb1tm1a(EUCOMM)Wtsi/Ieg from IMSR.
View all literature mentionsThis monoclonal targets CD335 (NKp46)
View all literature mentionsMus musculus with name B6Dnk;B6N-Setdb1tm1a(EUCOMM)Wtsi/Ieg from IMSR.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
scicrunch.org
