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  • br bioc html ChIPpeakAnno html br WebGestalt br

    2019-10-14


    bioc/html/ChIPpeakAnno.html
    WebGestalt
    http://www.webgestalt.org/
    FastQC
    Babraham Bioinformatics
    (http://www.bioinformatics.babraham.ac.uk/
    projects/fastqc/)
    https://github.com/marcelm/cutadapt
    PinAPL-Py webtool
    https://github.com/LewisLabUCSD/PinAPL-Py
    STRING mouse interactome
    https://string-db.org/
    https://pypi.org/project/visJS2jupyter/
    Seurat FindClusters
    https://github.com/satijalab/seurat
    SuperCT
    https://sct.lifegen.com/register
    BaseSpace
    Illumina
    https://www.basespace.illumina.com
    STAR aligner
    https://github.com/alexdobin/STAR
    National Institute of Health
    https://imagej.nih.gov/ij/download.html
    Leica
    https://leica-las-af-lite.software.informer.com/
    GraphPad Prism software version 7.0d
    GraphPad Software Inc.
    https://www.graphpad.com/scientiÞc-
    software/prism/
    cBioPortal
    cBioportal
    http://www.cbioportal.org
    Tree Star
    fjinstallers/FlowJo_9.9.6.zip
    Other (Equipment)
    Covaris S2 ultrasonicator
    Covaris Inc.
    Illumina
    Illumina
    NextSeq 500 system
    Illumina
    iCycler Real-Time PCR System
    Biorad
    Leica TCS SP5 II Confocal System
    Leica Microsystems
    Leica SP5 Confocal System
    Leica Microsystems
    FACSAria III
    Becton Dickinson
    CONTACT FOR REAGENT AND RESOURCE SHARING
    Further information and requests for resources and reagents should be directed to and will be fulÞlled by the Lead Contact, Tannish-tha Reya ([email protected]).
    EXPERIMENTAL MODEL AND SUBJECT DETAILS
    Mice
    listed above are immunocompetent, with the exception of RORg -knockout mice which are known to lack TH17 T Dynasore as described previously (Ivanov et al., 2006); these mice were maintained on antibiotic water (sulfamethoxazole and trimethoprim) when enrolled in ßank transplantation and drug studies as outlined below. Immune compromised NOD/SCID (NOD.CB17-Prkdcscid/J, Stock No:
    001303) and NSG (NOD.Cg-PrkdcscidIL2rgtm1Wji/SzJ, Stock No: 005557) mice purchased from The Jackson Laboratory. All mice were speciÞc-pathogen free, and bred and maintained in the animal care facilities at the University of California San Diego. Animals had access to food and water ad libitum, and were housed in ventilated cages under controlled temperature and humidity with a 12 hour light-dark cycle. All animal experiments were performed according to protocols approved by the University of California San Diego Institutional Animal Care and Use Committee. No sexual dimorphism was noted in all mouse models. Therefore, males and females of each strain were equally used for experimental purposes and both sexes are represented in all datasets. All mice enrolled in experimental studies were treatment-naive and not previously enrolled in any other experimental study. r> Both REM2-KPf/fC and WT-KPf/fC mice (REM2; LSL-KrasG12D/+; Trp53f/f; Ptf1a-Cre and LSL-KrasG12D/+, ; Trp53f/f; Ptf1a-Cre respectively) were used for isolation of tumor cells, establishment of primary mouse tumor cell and organoid lines, and autochtho-nous drug studies as described below. REM2-KPf/fC and KPf/fC mice were enrolled in drug studies between 8 to 11 weeks of age, and
    were used for tumor cell sorting and establishment of cell lines when isotonic reached end-stage disease between 10 and 12 weeks of age. REM2-KPf/fC mice were used for in vivo imaging studies between 9.5-10.5 weeks of age. KPR172HC (LSL-KrasG12D/+, ; Trp53R172h/+; Ptf1a-Cre) Dynasore mice were used for cell sorting and establishment of tumor cell lines when they reached end-stage disease