Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression and epigenetic events in specific cell types in a range of species, including postmortem human brain. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping and immunofluorescence localization. Studies of sixteen human postmortem brains revealed gender specific transcriptional differences, cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event evident in three donor samples. Our data establish a comprehensive approach for analysis of molecular events associated with specific circuits and cell types in a wide variety of human conditions.
Pubmed ID: 30320555 RIS Download
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Original 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 mentionsCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
View all literature mentionsOpen source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
View all literature mentionsCollection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.
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View all literature mentionsCell sorter features hardware and software enhancements that improve overall ease of use, flexibility,and aseptic capability. Offers new options in lasers and nozzles to support more advanced multicolor applications. Built on fixed alignment technology. FACSAria II cell sorter is first generation of BD FACSAria system where flow cell is in true fixed alignment with laser, to reduce startup time and improve reproducibility.
View all literature mentionsSoftware pipeline to process ATAC-Seq data. Used for automated end-to-end quality control and processing of ATAC-seq and DNase-seq data.
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View all literature mentionsMus musculus with name C57BL/6J from IMSR.
View all literature mentionsMus musculus with name B6;FVB-Tg(Ntsr1-EGFP/Rpl10a)TS16Htz/J from IMSR.
View all literature mentionsMus musculus with name B6.FVB(Cg)-Tg(Colgalt2-EGFP/Rpl10a)DU9Htz/J from IMSR.
View all literature mentionsMus musculus with name B6;FVB-Tg(Sept4-EGFP/Rpl10a)DS152Htz/J from IMSR.
View all literature mentionsMus musculus with name B6;FVB-Tg(Pcp2-EGFP/Rpl10a)DR168Htz/J from IMSR.
View all literature mentionsMus musculus with name B6;FVB-Tg(Neurod1-EGFP/Rpl10a)JP241Htz/J from IMSR.
View all literature mentionsThis polyclonal targets Human Olig2
View all literature mentionsThis unknown targets SorCS3
View all literature mentionsThis monoclonal targets NeuN
View all literature mentionsThis monoclonal targets MAG
View all literature mentionsThis monoclonal targets PDE1C (G-7)
View all literature mentionsThis polyclonal targets Mouse GFAP
View all literature mentionsThis unknown targets MOG
View all literature mentionsThis polyclonal targets EAAT1/SLC1A3 / GLAST1
View all literature mentions