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. 2023 Jun 3;30(7):1619–1635. doi: 10.1038/s41418-023-01168-3
REAGENT  or RESOURCE SOURCE IDENTIFIER
Antibodies
p53 Leica Biosystems Cat# NCL-L-p53-CM5p
iASPP Ascites LXO49.3
β-Tubulin Santa Cruz Cat# sc-5274
p21 Santa Cruz Cat# sc-471
Actin Santa Cruz Cat# sc-47778
Bax Cell Signaling Technology Cat# 2772 S
Cytokeratin 8 DHSB Cat# TROMA-I
Biotinylated Anti-Mouse antibody Vector Labs Cat# BA-9200-1.5
Biotinylated Anti-Rabbit antibody Vector Labs Cat# BA-1000-1.5
Biotinylated Anti-Rat antibody Vector Labs Cat# BA-9400-1.5
APC-Cy7 anti-CD3 (17A2) BioLegend Cat# 100221
PE-Cy5 anti-CD4 (RM4-5) BioLegend Cat# 100513
BV421 anti-CD4 (GK1.5) BioLegend Cat# 100437
FITC anti-CD4 (RM4-5) eBioscience Cat# 11-0042-82
APC anti-CD8α (53-6.7) BioLegend Cat# 100711
BV510 anti-CD8α (53-6.7) BioLegend Cat# 100751
BV785 anti-CD8α (53-6.7) BioLegend Cat# 100749
BV510 anti-CD11b (M1/70) BioLegend Cat# 101245
PerCP-Cy5.5 anti-CD11b (M1/70) BioLegend Cat# 101227
BV421 anti-CD11c (N418) BioLegend Cat# 117329
PE-Cy7 anti-CD11c (N418) BioLegend Cat# 117317
BV650 anti-CD19 (6D5) BioLegend Cat# 115541
BV510 anti-CD25 (PC61) BioLegend Cat# 102041
FITC anti-CD45 (30-F11) BioLegend Cat# 103107
PE/Dazzle 594 anti-CD49b (DX5) BioLegend Cat# 108923
PE-Cy7 anti-CD68 (FA-11) BioLegend Cat# 137015
BV421 anti-F4/80 (BM8) BioLegend Cat# 123131
BV711 anti-F4/80 (BM8) BioLegend Cat# 123147
BV785 anti-Ly6C (HK1.4) BioLegend Cat# 128041
PerCP-Cy5.5 anti-Ly6G (1A8) BioLegend Cat# 127615
Alexa Fluor 700 anti-MHCII (M5/114.15.2) BioLegend Cat# 107621
PE anti-TCRγδ (UC7-13D5) BioLegend Cat# 107507
Biological Samples
Tissue Microarray of Human Pancreatic Disease US Biomax Cat# PA2081b
Chemicals, peptides, and recombinant proteins
Rat Tail Collagen I Gibco Cat# A1048301
HBSS (10X) Gibco Cat# 14065056
RPMI 1640 Medium Gibco Cat# 11875093
Collagenase P Roche Cat# 11213857001
Soybean Trypsin Inhibitor (STI) Sigma-Aldrich Cat# T6522
Dexamethasone Sigma-Aldrich Cat# D4902
TGFα PeproTech Cat# 100-16 A
Caerulein Sigma-Aldrich Cat# C9026
Matrigel Basement Membrane Matrix Corning Cat# CLS356234
Nutlin-3a Sigma-Aldrich Cat# SML0580
Permeabilization Buffer eBioscience Cat# 00-8333-56
Critical Commercial Assays
Mouse Cytokine Array Panel A - Proteome Profiler R&D systems Cat# ARY006
RNeasy Mini Kit QIAGEN Cat# 74106
RNase-Free DNase Set QIAGEN Cat# 79254
QuantSeq FWD 3’ mRNA-Seq Library Prep Kit Lexogen Cat# 015
Deposited Data
Mouse pancreatic cell line RNA-seq This paper Raw data: deposited with GEO with accession GSE226595
Experimental Models: Cell lines
KC-1: Pdx1-Cre; KrasG12D/+; p53R172H/+; Sex Female This paper N/A
KC-2: Pdx1-Cre; KrasG12D/+; p53R172H/+; Sex Male This paper N/A
KC-3: Pdx1-Cre; KrasG12D/+; p53R172H/+; Sex Female This paper N/A
KC;iASPPΔ8/Δ8-1: Pdx1-Cre; KrasG12D/+; iASPPΔ8/Δ8; Sex Female This paper N/A
KC;iASPPΔ8/Δ8-2: Pdx1-Cre; KrasG12D/+; iASPPΔ8/Δ8; Sex Male This paper N/A
KC;iASPPΔ8/Δ8-3: Pdx1-Cre; KrasG12D/+; iASPPΔ8/Δ8; Sex Male This paper N/A
KC;iASPPΔ8/Δ8-4: Pdx1-Cre; KrasG12D/+; iASPPΔ8/Δ8; Sex Male This paper N/A
KPC-1: Pdx1-Cre; KrasG12D/+; p53R172H/+; Sex Male This paper N/A
KPC-2: Pdx1-Cre; KrasG12D/+; p53R172H/+; Sex Female This paper N/A
KPC-3: Pdx1-Cre; KrasG12D/+; p53R172H/+; Sex Female This paper N/A
KPC-4: Pdx1-Cre; KrasG12D/+; p53R172H/+; Sex Male This paper N/A
KPC;iASPPΔ8/Δ8-1: Pdx1-Cre; KrasG12D/+; p53R172H/+; iASPPΔ8/Δ8; Sex Male This paper N/A
KPC;iASPPΔ8/Δ8-2: Pdx1-Cre; KrasG12D/+; p53R172H/+; iASPPΔ8/Δ8; Sex Female This paper N/A
KPC;iASPPΔ8/Δ8-3: Pdx1-Cre; KrasG12D/+; p53R172H/+; iASPPΔ8/Δ8; Sex Male This paper N/A
KPC;iASPPΔ8/Δ8-4: Pdx1-Cre; KrasG12D/+; p53R172H/+; iASPPΔ8/Δ8; Sex Male This paper N/A
KPC;iASPPΔ8/Δ8-5: Pdx1-Cre; KrasG12D/+; p53R172H/+; iASPPΔ8/Δ8; Sex Male This paper N/A
Experimental Models: Organisms/Strains
Mouse: C57BL/6J females (6-8 weeks) Envigo Cat# 57
Mouse: Athymic Nude-Foxn1nu (6-8 weeks) Envigo Cat# 69
Mouse: KC; Pdx1-Cre; KrasLSL-G12D/+ [23] N/A
Mouse: KPC; Pdx1-Cre; KrasLSL-G12D/+; p53R172H/+ [26] N/A
Mouse: iASPPΔ8/Δ8 [37] N/A
Mouse: KC;iASPPΔ8/Δ8; Pdx1-Cre; KrasLSL-G12D/+; iASPPΔ8/Δ8 This paper N/A
Mouse: KPC;iASPPΔ8Δ8; Pdx1-Cre; KRAS+/LSL-G12D; p53R172H/+; iASPPΔ8/Δ8 This paper N/A
Software and Algorithms
GraphPad Prism 8.3 GraphPad Prism Software https://www.graphpad.com/scientific-software/prism/
NDP.scan version 2.8.24 Hamamatsu, Japan https://www.hamamatsu.com/eu/en/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html
NDP.view2 version 2.8.24 Hamamatsu, Japan https://www.hamamatsu.com/eu/en/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html
FlowJo FlowJo https://www.flowjo.com/solutions/flowjo/downloads
Enrichr Ma’ayan Lab https://maayanlab.cloud/Enrichr/
TCGABiolinks 2.24.3 Bioconductor R package https://academic.oup.com/nar/article/44/8/e71/2465925?login=true
edgeR 3.38.0 Bioconductor R package https://academic.oup.com/bioinformatics/article/26/1/139/182458?login=true
GSVA 1.44.0 Bioconductor R package https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-7
Cluster 2.1.3 CRAN https://cran.r-project.org/web/packages/cluster/cluster.pdf
Survival 3.3-1 CRAN https://link.springer.com/book/10.1007/978-1-4757-3294-8
Survminer 0.4.9 CRAN https://rpkgs.datanovia.com/survminer/index.html
R 4.2.1 Vienna, Austria https://www.R-project.org/
DESeq2 CRAN https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8
pheatmap CRAN https://CRAN.R-project.org/package=pheatmap
EnhancedVolcano Github https://github.com/kevinblighe/EnhancedVolcano
ashr CRAN 10.1093/biostatistics/kxw041