Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Other | Matrigel | Corning | 356231 | Growth-factor-reduced for organoid growth. |
| Other | TrypLE Express | Gibco | 12605–028 | For organoid dissociation during passaging. |
| Other | Stem Pro Accutase | Gibco | A11105-01 | For organoid dissociation during passaging. |
| Other | CryoStor CS10 stem cell freezing medium | STEMCell Technologies | 07930 | For organoid cryopreservation. |
| Other | Trypsin-250 | Alfa Aesar | Alfa Aesar | For stem cell isolation from tissue. |
| Other | Collagenase V | Sigma-Aldrich | C9263-100MG | For stem cell isolation from tissue. |
| Other | recombinant human EGF | Gibco | PHG0314 | For organoid growth media. |
| Other | recombinant human R-spondin 1 | R & D systems | 4645-RS-100 | For organoid growth media. |
| Other | recombinant human FGF2 | Peprotech | 100–18 C | For organoid growth media. |
| Other | recombinant human HGF | Peprotech | 100–39 | For organoid growth media. |
| Other | ITS-X supplement | Gibco | 51500–056 | For organoid growth media. |
| Other | KO serum replacement | ThermoFisher | 10828010 | For organoid growth media. |
| Other | NRG1 | Cell Signaling | 5218SC | For organoid growth media. |
| Other | A83-01 | Tocris | 2939 | For organoid growth media. |
| Other | Y27632 | Sigma or STEMCell Technologies | Y0503 or 72304 | For organoid growth media. |
| Other | nicotinamide | Sigma | N0636 | For organoid growth media. |
| Other | FBS | Cytiva HyClone | SH30070.03 | For organoid growth media. Heat inactivated at 50 oC for 30 min. |
| Other | Advanced DMEM/F12 medium | Life Technologies | 12634–010 | For organoid growth media. |
| Other | 24-well tissue culture plates | Corning | 3526 | For organoid plating. |
| Cell line (human) | HEK-Blue IFN-λ reporter cells | InvivoGen | hkb-ifnl | |
| Other | HCMV AD169r BADrUL131-Y4 | T. Shenk | PMID: 16051825 | |
| Other | HCMV TB40/E | N. Moorman | PMID: 21307184 | |
| Other | 8-well chamber slide | Millipore | PEZGS0816 | For organoid plating. |
| Other | Cell recovery solution | Corning | 354253 | |
| Other | Vectashield | Vector Laboratories | H-1200–10 | Mounting medium for immunofluorescence. |
| Antibody | Mouse monoclonal Cytokeratin-19 | Abcam | ab9221 | (Immunofluorescence, 1:500) |
| Antibody | Rabbit monoclonal Cytokeratin-19 | Abcam | ab52625 | (Immunofluorescence, 1:500) |
| Antibody | Rabbit polyclonal E-cadherin | Invitrogen | PA5-85088 | (Immunofluorescence, 1:500) |
| Antibody | Rabbit monoclonal EpCAM | Abcam | ab223582 | (Immunofluorescence, 1:500) |
| Antibody | Mouse monoclonal Mucin 5AC | Abcam | ab3649 | (Immunofluorescence, 1:500) |
| Antibody | Rabbit polyclonal SIGLEC6 | Abcam | ab262851 | (Immunofluorescence, 1:500) |
| Antibody | Mouse monoclonal HLA-G | Abcam | ab52454 | (Immunofluorescence, 1:500) |
| Antibody | Rabbit monoclonal HLA-G | Abcam | ab283260 | (Immunofluorescence, 1:500) |
| Antibody | Mouse monoclonal Ki67 | BD Biosciences | 550609 | (Immunofluorescence, 1:500; Immunohistochemistry, 1:200) |
| Antibody | Rabbit monoclonal SDC-1 | Abcam | ab128936 | (Immunofluorescence, 1:500) |
| Other | Alexa Fluor 594–conjugated phalloidin | Invitrogen | A12381 | For actin staining. (Immunofluorescence 1:1000) |
| Other | Alexa Fluor 633–conjugated phalloidin | Invitrogen | A22284 | For actin staining. (Immunofluorescence 1:1000) |
| Other | Alexa Fluor Plus 488 Goat anti-Mouse IgG secondary antibody | Invitrogen | A32723 | Secondary antibody for immunofluorescence. (Immunofluorescence 1:1000) |
| Other | Alexa Fluor 594 Goat anti-Mouse IgG secondary antibody | Invitrogen | A11032 | Secondary antibody for immunofluorescence. (Immunofluorescence 1:1000) |
| Other | Alexa Fluor 488 Goat anti-Rabbit IgG secondary antibody | Invitrogen | A11034 | Secondary antibody for immunofluorescence. (Immunofluorescence 1:1000) |
| Other | Alexa Fluor 594 Goat anti-Rabbit IgG secondary antibody | Invitrogen | A11037 | Secondary antibody for immunofluorescence. (Immunofluorescence 1:1000) |
| Software, algorithm | Fiji | N/A | https://imagej.net/software/fiji/ | For image analysis, including three- dimensional reconstructions. |
| Software, algorithm | CellSens | Olympus | N/A | |
| Software, algorithm | Imaris | Oxford Instruments | Version 9.2.; for image analysis, including three- dimensional reconstructions. |
|
| Software, algorithm | CLC Genomics | Qiagen | Version 20 | |
| Software, algorithm | GraphPad Prism | Dotmatics | Version 9 | |
| Other | Vectastain Elite ABC HRP Kit | Vector Laboratories | PK-6100 | For immunohistochemistry. |
| Other | Biotinylated Goat Anti-Rabbit | Vector Laboratories | BA-1000 | For immunohistochemistry. (Immunohistochemistry, 1:250) |
| Other | Biotinylated Goat Anti-Mouse | Vector Laboratories | BA-9200 | For immunohistochemistry. (Immunohistochemistry, 1:250) |
| Other | DAB substrate | Vector Laboratories | SK-4100 | For immunohistochemistry. |
| Other | Vectamount Permanent Mounting Medium | Vector Laboratories | H-5000 | For immunohistochemistry. |
| Commercial assay, kit | GenElute total mammalian RNA miniprep kit | Sigma | RTN70-1KT | With on-column DNAse treatment |
| Commercial assay, kit | iScript cDNA synthesis kit | Biorad | 1708891 | N/A |
| Commercial assay, kit | iQ SYBR Green Supermix | Biorad | 1708882 | N/A |
| Software, algorithm | DeSeq2 | M.Love et al | PMID: 25516281 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Software, algorithm | pheatmap | Raivo Kolde | https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf | |
| Software, algorithm | pcaExplorer | Marini and Binder | PMID: 31195976 | https://bioconductor.org/packages/release/bioc/html/pcaExplorer.html |
| Commercial assay, kit | Bio-Plex Pro Human Inflammation Panel 1 | Biorad | 171AL001M | |
| Commercial assay, kit | Bio-Plex Human Chemokine Panel, 40-plex | Biorad | 171AK99MR2 | |
| Commercial assay, kit | Bio-Plex Pro Human Cytokine Screening Panel, 48-Plex kit | Biorad | 12007283 | |
| Commercial assay, kit | hCG Human ProcartaPlex Simplex Kit | Thermo Fisher | EPX010-12388-901 | |
| Commercial assay, kit | CA125/Mucin-16 Human ProcartaPlex Simplex Kit | Thermo Fisher | EPX010-12437-901 | |
| Chemical compound, drug | Poly(I:C) HMW | Invivogen | tlrl-pic | |
| Chemical compound, drug | Ruxolitinib | Invivogen | tlrl-rux | |
| Biological sample | Primary human trophoblasts from full term placentas | PMID: 27066743 | SRP067137 | Bulk RNASeq from primary human trophoblasts. |
| Biological sample | Primary human trophoblasts from full term placentas | PMID: 28784796 | SRP109039 | Bulk RNASeq from primary human trophoblasts. |
| Biological sample | First trimester placental tissue | University of Cambridge | PRJEB38810 | Bulk RNASeq from first trimester placental tissue. |
| Biological sample | Full-term placental tissue | PMID: 33969332 | PRJNA721668 | Bulk RNASeq from ffull-term placental tissue. |