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 |