br bioc html ChIPpeakAnno html br WebGestalt br

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) mice were used for cell sorting and establishment of tumor cell lines when they reached end-stage disease