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picard 'markduplicate' command line utility  (Broad Institute Inc)
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Picard 'Markduplicate' Command Line Utility, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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prism 8 v8.1.2  (GraphPad Software Inc)
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KEY RESOURCES TABLE
Prism 8 V8.1.2, supplied by GraphPad Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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KEY RESOURCES TABLE

Journal: Neuron

Article Title: Inhibition of Upf2-Dependent Nonsense-Mediated Decay Leads to Behavioral and Neurophysiological Abnormalities by Activating the Immune Response

doi: 10.1016/j.neuron.2019.08.027

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: RNAi of Upf2: y1 v1; P {TRiP.JF01560}attP2 Bloomington Drosophila Stock Center BDSC: 31095 FlyBase: FBst0031095 D. melanogaster: elav -GAL4: P{GAL4-elav.L} Bloomington Drosophila Stock Center BDSC: 8765 FLyBase: FBtp0000743 Upf2 conditional knockout mice Weischenfeldt et al., 2008 Upf2 floxed/floxed CamKII-Cre mice The Jackson Laboratory JAX: 027400 Oligonucleotides See Table S5 for the list of oligos N/A Software and Algorithms Prism 8 v8.1.2 GraphPad https://www.graphpad.com/scientific-software/prism/ FreezeView Software Actimetrics https://www.coulbourn.com/category_s/277.htm Image Lab Software v6.0.1 Bio-Rad https://www.bio-rad.com/en-us/product/image-lab-software?lD=KRE6P5E8Z PANTHER v12.0 Tang and Thomas, 2016 http://www.pantherdb.org Avisoft SASLab Pro V5.2.13 Avisoft Bioacoustics http://www.avisoft.com/soundanalysis.htm CodonCode Aligner CodonCode Corporation https://www.codoncode.com/aligner/ Novoalign v3.02.00 Novooraft Technologies http://www.novocraft.com/products/novoalign/ MarkDuplioates (Picard) Broad Institute https://broadinstitute.github.io/picard/command-line-overview.html FastQC Babraham Institute https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ STAR aligner v2.5.3a Cold Spring Harbor Laboratories https://github.com/alexdobin/STAR Trim Galore Babraham Institute https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ RUVSeq v1.16.1 Bioconductor https://bioconductor.org/packages/release/bioc/html/RUVSeq.html StepOne™ Software Applied Biosystem (Life Technology-ThermoFisher Scientific) https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/StepOne-and-StepOnePlus-Real-Time-PCR-System.html DESeq2 v1.22.2 European Molecular Biology Laboratory https://bioconductor.org/packages/release/bioc/html/DESeq2.html KaryoStudio Software Illumina https://support.illumina.com/downloads/karyostudio_software_v14.html RSubread Package v1.5.2 The Walter and Eliza Hall Institute of Medical Research http://subread.sourceforge.net Open in a separate window KEY RESOURCES TABLE Humans carrying novel variants in UPF2 exhibit speech and language deficits Upf2-deficient mice and flies have impaired NMD and exhibit behavioral deficits Inhibition of Upf2-dependent NMD triggers immune activation in mice Reduction of brain inflammation reverses synaptic and behavioral deficits

Techniques: Recombinant, Sequencing, SYBR Green Assay, Multiplex Assay, Microarray, Knock-Out, Software