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. 2024 Nov 19;27(12):111417. doi: 10.1016/j.isci.2024.111417
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

anti-CD31/PECAM-1 antibody (H-3) Santa Cruz Biotechnology sc-376764
anti-ESM1 Abcam ab235966
goat anti-mouse Alexa Fluor 488 Invitrogen A-11001
donkey anti-rabbit Alexa Fluor 647 Invitrogen A-31573

Chemicals, peptides, and recombinant proteins

M199 medium Gibco Cat#22350-029
L-glutamine Gibco Cat#35050-061
Endothelial Cell Growth Supplement (ECGS)/Heparin PromoCell Cat#C-30120
fetal bovine serum Sigma Cat#F7524
SpCas9 IDT Cat#1081059
Opti-MEM Thermo Scientific Cat#31985062
AccuPrime PFX Reaction Mix Invitrogen Cat#92008
methylcellulose Merck Cat#M05129
Collagen-type I solution Merck Cat#08-115
4% paraformaldehyde AH Diagnostics Cat#SC-281692

Critical commercial assays

NucleoSpin Gel and PCR Clean-up kit Macherey Cat#2006/001
Mix2Seq Kit Eurofins Genomics N/A

Experimental models: Cell lines

Human umbilical vein endothelial cells (HUVECs) Isolated from human umbilical vein, this study N/A

Oligonucleotides

LAMA4 gRNA (spacer sequences): TGACATTGAAGGGAGCTCAG Synthego, US N/A
TGFB1 gRNA (spacer sequences): GGCACCTCCCCCTGGCTCG Synthego, US N/A
TGFBR1 gRNA (spacer sequences): TTGACTTAATTCCTCGAGAT Synthego, US N/A

Software and algorithms

Seurat https://satijalab.org/seurat/ version 4.1.0
cNMF https://github.com/dylkot/cNMF version 1.3.5
Monocle2 https://cole-trapnell-lab.github.io/monocle-release/ version 2.22.0
harmony https://github.com/immunogenomics/harmony version 0.1.0
org.Hs.eg.db https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html version 3.16.0
clusterProfiler https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html version 4.6.0
ggplot2 https://ggplot2.tidyverse.org/ version 3.3.5
GSVA https://bioconductor.org/packages/release/bioc/html/GSVA.html version 1.46.0
pheatmap https://www.rdocumentation.org/packages/pheatmap/versions/1.0.12/topics/pheatmap version 1.0.12
PROGENy https://github.com/saezlab/progeny version 1.16.0
pyscenic https://github.com/aertslab/pySCENIC version 0.11.2
CellChat https://github.com/sqjin/CellChat version 1.5.0
CIBERSORTx https://cibersortx.stanford.edu/ version 0.1.0
ImageJ https://imagej.net/ij/ version 2.9.0
Code availability https://github.com/lianglangchao/ovarian_cancer_llc_V2 N/A
Ovarian cancer single cell RNA expression database https://dreamapp.biomed.au.dk/OvaryCancer_DB/ N/A
Integrated OC scRNA-seq data https://lambrechtslab.sites.vib.be/en/pan-cancer-blueprint-tumor-microenvironment-0 N/A
Integrated OC scRNA-seq data https://lambrechtslab.sites.vib.be/en/high-grade-serous-tubo-ovarian-cancer-refined-single-cell-rna-sequencing-specific-cell-subtypes N/A
Integrated OC scRNA-seq data https://github.com/vicDRC/CCR_CD39study/tree/master/data N/A
Integrated OC scRNA-seq data Gene Expression Omnibus (GEO) GSE140819
GSE173682
GSE165897
GSE178101
GSE151214
GSE150443
GSE151316
GSE184880
GSE160755
GSE193371
GSE194105
GSE154600
GSE130000
GSE158937

Other

Nikon laser confocal microscope Japan A1 HD25