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Dendritic cells (DCs) play a critical role in orchestrating adaptive immune responses due to their unique ability to initiate T cell responses and direct their differentiation into effector lineages. Classical DCs have been divided into two subsets, cDC1 and cDC2, based on phenotypic markers and their distinct abilities to prime CD8 and CD4 T cells. While the transcriptional regulation of the cDC1 subset has been well characterized, cDC2 development and function remain poorly understood. By combining transcriptional and chromatin analyses with genetic reporter expression, we identified two principal cDC2 lineages defined by distinct developmental pathways and transcriptional regulators, including T-bet and RORγt, two key transcription factors known to define innate and adaptive lymphocyte subsets. These novel cDC2 lineages were characterized by distinct metabolic and functional programs. Extending our findings to humans revealed conserved DC heterogeneity and the presence of the newly defined cDC2 subsets in human cancer.
Pubmed ID: 31668803
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A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading.
View all literature mentionsOriginal SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsNetwork of ftp and web servers around world that store identical, up to date, versions of code and documentation for R. Package archive network for R programming language.
View all literature mentionsWeb based service that offers software developers centralized online location to control and manage free and open source software projects. Open source software tool and business public software platform.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role.
View all literature mentionsWeb based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress.
View all literature mentionsSoftware repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
View all literature mentionsCommercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.
View all literature mentionsSoftware for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.
View all literature mentionsA commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis.
View all literature mentionsAn Organization portal, Antibody supplier, Service resource,
View all literature mentionsAmerican chemical, life science and biotechnology company owned by Merck KGaA. Merger of Sigma Chemical Company and Aldrich Chemical Company. Provides organic and inorganic chemicals, building blocks, reagents, advanced materials and stable isotopes for chemical synthesis, medicinal chemistry and materials science, antibiotics, buffers, carbohydrates, enzymes, forensic tools, hematology and histology, nucleotides, proteins, peptides, amino acids and their derivatives.
View all literature mentionsSoftware tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.
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 mentionsHuman and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.
View all literature mentionsProcedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. The algorithm uses cyclical coordinate descent in a path-wise fashion.
View all literature mentionsGraph-based alignment of next generation sequencing reads to a population of genomes.
View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsSoftware tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.
View all literature mentionsSoftware R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.
View all literature mentionsSoftware R package to measure reproducibility of findings identified from replicate experiments and to provide highly stable thresholds based on reproducibility.
View all literature mentionsSoftware package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis.
View all literature mentionsAn independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels.
View all literature mentionsAllele Detail: Targeted, Transgenic This is a legacy resource.
View all literature mentionsThis monoclonal targets Ly-6C
View all literature mentionsThis monoclonal targets CD274
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets CD371
View all literature mentionsThis monoclonal targets MHC Class II
View all literature mentionsThis monoclonal targets ESAM
View all literature mentionsThis monoclonal targets CD115
View all literature mentionsThis monoclonal targets CX3CR1
View all literature mentionsThis monoclonal targets CD45R (B220)
View all literature mentionsThis monoclonal targets NK1.1
View all literature mentionsThis monoclonal targets Ly-6C
View all literature mentionsThis monoclonal targets CD86 (B7-2)
View all literature mentionsThis monoclonal targets CD45
View all literature mentionsThis monoclonal targets CD301
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets TCR beta chain
View all literature mentionsThis monoclonal targets CD4
View all literature mentionsThis monoclonal targets HLA-DR
View all literature mentionsThis monoclonal targets CD49b
View all literature mentionsThis monoclonal targets IFN gamma
View all literature mentionsThis monoclonal targets CD11c
View all literature mentionsThis monoclonal targets CD45.1
View all literature mentionsThis monoclonal targets CLEC4A
View all literature mentionsThis monoclonal targets IL-17A
View all literature mentionsThis monoclonal targets XCR1
View all literature mentionsThis monoclonal targets CD14
View all literature mentionsThis monoclonal targets CD90.1 (Thy-1.1)
View all literature mentionsThis monoclonal targets CD135 (Flt3)
View all literature mentionsThis monoclonal targets CD3e
View all literature mentionsThis monoclonal targets CD3
View all literature mentionsThis monoclonal targets CD4
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets XCR1
View all literature mentionsThis monoclonal targets Ly-6G
View all literature mentionsThis monoclonal targets CD123
View all literature mentionsThis monoclonal targets CD3epsilon
View all literature mentionsThis monoclonal targets XCR1
View all literature mentionsThis monoclonal targets CD11c
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets FOXP3
View all literature mentionsThis monoclonal targets CD16 / CD32
View all literature mentionsThis monoclonal targets CD64
View all literature mentionsThis monoclonal targets Siglec H
View all literature mentionsThis monoclonal targets CD56
View all literature mentionsThis monoclonal targets HLA-DR
View all literature mentionsThis monoclonal targets CD11b
View all literature mentionsThis monoclonal targets CD11c
View all literature mentionsThis monoclonal targets IL-4
View all literature mentionsThis monoclonal targets CD14
View all literature mentionsThis monoclonal targets Siglec-F
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets Axl
View all literature mentionsThis monoclonal targets CD90.2
View all literature mentionsThis monoclonal targets CD117 (c-Kit)
View all literature mentionsThis monoclonal targets TER-119
View all literature mentionsThis monoclonal targets CD56
View all literature mentionsThis monoclonal targets XCR1
View all literature mentionsThis monoclonal targets CD45
View all literature mentionsThis monoclonal targets CD19
View all literature mentionsThis monoclonal targets TCR beta chain
View all literature mentionsThis monoclonal targets CD301
View all literature mentionsThis monoclonal targets CD45.2
View all literature mentionsThis monoclonal targets major hematopoietic cell lineages
View all literature mentionsThis monoclonal targets CD44
View all literature mentionsThis monoclonal targets Fc epsilon RI alpha
View all literature mentionsThis monoclonal targets CD3
View all literature mentionsThis monoclonal targets CD62L
View all literature mentionsThis monoclonal targets CD64
View all literature mentionsThis monoclonal targets CD90.2 (Thy-1.2)
View all literature mentionsThis monoclonal targets CD1c
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Mus musculus with name B6.SJL-Ptprca Pepc
Mus musculus with name C57BL/6J from IMSR.
View all literature mentionsMus musculus with name B6.Cg-Gt(ROSA)26Sortm3(CAG-EYFP)Hze/J from IMSR.
View all literature mentionsStatistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
View all literature mentionsMus musculus with name B6.Cg-Tg(TcraTcrb)425Cbn/J from IMSR.
View all literature mentionsMus musculus with name B6.FVB-Tg(Rorc-cre)1Litt/J from IMSR.
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