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  • br Anti BrdU APC br Anti Annexin V APC

    2019-10-14


    Anti-BrdU-APC
    Anti-Annexin V-APC
    Bacterial and Virus Strains
    Chemically competent One shot Stbl3
    Biological Samples
    Patient-derived pancreatic cancer Moores Cancer Center, N/A
    xenografts and organoid lines University Y-27632 California
    San Diego
    Chemicals, Peptides, and Recombinant Proteins
    Gemcitabine Sigma Cat# G6423
    Critical Commercial Assays
    NEBNext Ultra II DNA library prep kit
    NucleoBond Xtra Maxi DNA puriÞcation kit
    KAPA HiFi HotStart ReadyMIX
    KAPA Biosystems Cat# KK2602
    QIAGEN Blood and Cell Culture DNA Midi Kit
    Chromium Single Cell 30 GEM library and
    gel bead kit v2
    RNeasy Micro Plus kit
    QIAGEN
    IlluminaÕs TruSeq Stranded mRNA Sample Illumina
    Prep Kit
    (Continued on next page)
    Continued
    REAGENT or RESOURCE SOURCE IDENTIFIER
    NEBNext Ultra II Directional RNA Library
    New England Biolabs
    Prep Kit for Illumina
    Superscript III
    Invitrogen
    Deposited Data
    https://www.ncbi.nlm.nih.gov/geo/
    ChIP-seq data
    Custom code for CRISPR screen analysis
    https://github.com/ucsd-ccbb/
    Primary Msi2+ and Msi2- KPf/fC RNA-seq data
    crispr_network_analysis.
    https://www.ncbi.nlm.nih.gov/geo/
    Genome-wide CRISPR screen data
    https://www.ncbi.nlm.nih.gov/geo/
    shRorc versus shControl KPf/fC RNA-seq data
    https://www.ncbi.nlm.nih.gov/geo/
    shRorc versus shControl KPf/fC H3K27ac
    https://www.ncbi.nlm.nih.gov/geo/
    ChIP-seq data
    sgRorc versus sgNT human PDAC FG RNA-seq
    https://www.ncbi.nlm.nih.gov/geo/
    Single-cell sequencing of KPR172HC tumors
    https://www.ncbi.nlm.nih.gov/geo/
    Single-cell sequencing of KPf/fC tumors
    https://www.ncbi.nlm.nih.gov/geo/
    Experimental Models: Cell Lines
    American Type Culture Collection
    Human: FG Cells
    Gifted by Dr. Andrew Lowy,
    This paper
    Mouse: KPf/fC
    This paper
    Mouse: REM2-KPf/fC
    This paper
    Experimental Models: Organisms/Strains
    The Jackson Laboratory
    The Jackson Laboratory
    The Jackson Laboratory
    Rorctm1Litt/J
    Mouse: REM2 (Msi2eGFP/+) reporter
    Mouse: NOD/SCID; NOD.CB17-Prkdcscid/J
    Dr. Tyler Jacks
    The Jackson Laboratory
    Mouse: NSG; NOD.Cg-PrkdcscidIL2rgtm1Wji/SzJ
    The Jackson Laboratory
    Oligonucleotides
    shRNA Autosomes targeting sequences- see Table S7
    This paper
    All primer sequences, see Table S7
    This paper
    Recombinant DNA
    mouse GeCKO CRISPRv2 knockout
    pooled library
    pRSV/REV
    pMDLg/pRRE
    (Continued on next page)
    Continued
    REAGENT or RESOURCE SOURCE
    IDENTIFIER
    pHCMVG
    pLV-hU6-mPGK-red
    Biosettia
    Software and Algorithms
    Kallisto
    https://pachterlab.github.io/kallisto/
    DESeq2
    https://bioconductor.org/packages/
    release/bioc/html/DESeq2.html
    Limma
    http://bioconductor.org/packages/
    release/bioc/html/limma.html
    Gene Set Enrichment Analysis (GSEA)
    http://software.broadinstitute.org/
    gsea/index.jsp
    Bioconductor GSVA
    https://bioconductor.org/packages/
    release/bioc/html/GSVA.html
    Langmead and Salzberg, 2012
    https://sourceforge.net/projects/bowtie-
    https://sourceforge.net/projects/samtools/
    Broad Institute
    https://broadinstitute.github.io/picard/
    Aaron Quinlan Lab
    https://github.com/genomecuration/JAMg/
    SICER-df algorithm version 1.1
    https://home.gwu.edu/ wpeng/Software.htm
    Tophat2
    https://ccb.jhu.edu/software/tophat/index.shtml
    Cufßinks, Cuffdiff
    http://cole-trapnell-lab.github.io/cufßinks/manual/
    ChippeakAnno
    http://bioconductor.org/packages/release/