Neutralization:Article Title: High-throughput histopathology for complex in vitro models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER CytoOne Multiwell Plates Star-Lab CC7682-7524 10% Formalin Sigma-Aldrich HT501320 SuperFrost Ultra Plus Gold Adhesion slides Fisher Scientific 11976299 TeloCol-6 Advanced BioMatrix 5225 Neutralization Solution For TeloCol-6 Advanced BioMatrix 5229 Collagen Rat Tail Type 1 Advanced BioMatrix 5153-1KIT Tris-EDTA buffer, pH 7.8 Ventana #950-227 Discovery Inhibitor Ventana #760-4840 Discovery Ab diluent Ventana #760-108 OmniMap anti-Rabbit HRP Ventana #760-4311 OmniMap anti-Mouse HRP Ventana #760-4310 OmniMap anti-Rat HRP Ventana #760-4457 Discovery ChromoMap DAB Kit Ventana #760-159 Hematoxylin II Ventana #790-2208 Bluing Reagent Ventana #760-2037 Alcohol Roche #CAS64-17-5 Xylol ACROS Organics #444240050 Standard histoglue Pertex #00811-EX DISCOVERY Ab Diluent Ventana 760–108 DISCOVERY Inhibitor Ventana 760–4840 DISCOVERY Goat Ig Block Ventana 760–6008 OmniMap anti-Ms HRP Ventana 760–4310 OmniMap anti-Rb HRP Ventana 760–4311 OmniMap anti-Goat HRP Ventana 760–4647 OmniMap anti-Rat HRP Ventana 760–4457 QD DAPI Ventana 760–4196 ULTRA LCS Ventana 650–210 Discovery CC1 Ventana 950–500 ULTRA LCS Buffer Ventana 950–223 Reaction Buffer Concentrate (10X) Ventana 950–300 DISCOVERY Wash Ventana 950–510 Tris-EDTA buffer pH 7.8 (CC1) Ventana #950-227 Discovery Inhibitor Ventana #760-4840 1X Plus Automation Amplification Diluent Akoya #FP1609 ProLongTM Gold Antifade Mountant Invitrogen #P36930 Mayer’s hemalum solution Sigma-Aldrich 109249 Critical commercial assays Gene imaging kit Vizgen 10400006 Cell Boundary Staining Vizgen 10400118 Merscope FFPE Sample Preparation reagents Vizgen 10400114 Merscope FFPE Slide Vizgen 10500102 1x Automation Amplification Diluent Akoya FP1609 Opal 480 Reagent Pack Akoya FP1500001KT Opal 520 Reagent Pack Akoya FP1487001KT Opal 570 Reagent Pack Akoya FP1488001KT Opal 620 Reagent Pack Akoya FP1495001KT Opal 690 Reagent Pack Akoya FP1497001KT (Continued on next page) Cell Reports Methods 6, 101419, June 15, 2026 e2 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS
Blocking Assay:Article Title: High-throughput histopathology for complex in vitro models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER CytoOne Multiwell Plates Star-Lab CC7682-7524 10% Formalin Sigma-Aldrich HT501320 SuperFrost Ultra Plus Gold Adhesion slides Fisher Scientific 11976299 TeloCol-6 Advanced BioMatrix 5225 Neutralization Solution For TeloCol-6 Advanced BioMatrix 5229 Collagen Rat Tail Type 1 Advanced BioMatrix 5153-1KIT Tris-EDTA buffer, pH 7.8 Ventana #950-227 Discovery Inhibitor Ventana #760-4840 Discovery Ab diluent Ventana #760-108 OmniMap anti-Rabbit HRP Ventana #760-4311 OmniMap anti-Mouse HRP Ventana #760-4310 OmniMap anti-Rat HRP Ventana #760-4457 Discovery ChromoMap DAB Kit Ventana #760-159 Hematoxylin II Ventana #790-2208 Bluing Reagent Ventana #760-2037 Alcohol Roche #CAS64-17-5 Xylol ACROS Organics #444240050 Standard histoglue Pertex #00811-EX DISCOVERY Ab Diluent Ventana 760–108 DISCOVERY Inhibitor Ventana 760–4840 DISCOVERY Goat Ig Block Ventana 760–6008 OmniMap anti-Ms HRP Ventana 760–4310 OmniMap anti-Rb HRP Ventana 760–4311 OmniMap anti-Goat HRP Ventana 760–4647 OmniMap anti-Rat HRP Ventana 760–4457 QD DAPI Ventana 760–4196 ULTRA LCS Ventana 650–210 Discovery CC1 Ventana 950–500 ULTRA LCS Buffer Ventana 950–223 Reaction Buffer Concentrate (10X) Ventana 950–300 DISCOVERY Wash Ventana 950–510 Tris-EDTA buffer pH 7.8 (CC1) Ventana #950-227 Discovery Inhibitor Ventana #760-4840 1X Plus Automation Amplification Diluent Akoya #FP1609 ProLongTM Gold Antifade Mountant Invitrogen #P36930 Mayer’s hemalum solution Sigma-Aldrich 109249 Critical commercial assays Gene imaging kit Vizgen 10400006 Cell Boundary Staining Vizgen 10400118 Merscope FFPE Sample Preparation reagents Vizgen 10400114 Merscope FFPE Slide Vizgen 10500102 1x Automation Amplification Diluent Akoya FP1609 Opal 480 Reagent Pack Akoya FP1500001KT Opal 520 Reagent Pack Akoya FP1487001KT Opal 570 Reagent Pack Akoya FP1488001KT Opal 620 Reagent Pack Akoya FP1495001KT Opal 690 Reagent Pack Akoya FP1497001KT (Continued on next page) Cell Reports Methods 6, 101419, June 15, 2026 e2 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS
Amplification:Article Title: High-throughput histopathology for complex in vitro models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER CytoOne Multiwell Plates Star-Lab CC7682-7524 10% Formalin Sigma-Aldrich HT501320 SuperFrost Ultra Plus Gold Adhesion slides Fisher Scientific 11976299 TeloCol-6 Advanced BioMatrix 5225 Neutralization Solution For TeloCol-6 Advanced BioMatrix 5229 Collagen Rat Tail Type 1 Advanced BioMatrix 5153-1KIT Tris-EDTA buffer, pH 7.8 Ventana #950-227 Discovery Inhibitor Ventana #760-4840 Discovery Ab diluent Ventana #760-108 OmniMap anti-Rabbit HRP Ventana #760-4311 OmniMap anti-Mouse HRP Ventana #760-4310 OmniMap anti-Rat HRP Ventana #760-4457 Discovery ChromoMap DAB Kit Ventana #760-159 Hematoxylin II Ventana #790-2208 Bluing Reagent Ventana #760-2037 Alcohol Roche #CAS64-17-5 Xylol ACROS Organics #444240050 Standard histoglue Pertex #00811-EX DISCOVERY Ab Diluent Ventana 760–108 DISCOVERY Inhibitor Ventana 760–4840 DISCOVERY Goat Ig Block Ventana 760–6008 OmniMap anti-Ms HRP Ventana 760–4310 OmniMap anti-Rb HRP Ventana 760–4311 OmniMap anti-Goat HRP Ventana 760–4647 OmniMap anti-Rat HRP Ventana 760–4457 QD DAPI Ventana 760–4196 ULTRA LCS Ventana 650–210 Discovery CC1 Ventana 950–500 ULTRA LCS Buffer Ventana 950–223 Reaction Buffer Concentrate (10X) Ventana 950–300 DISCOVERY Wash Ventana 950–510 Tris-EDTA buffer pH 7.8 (CC1) Ventana #950-227 Discovery Inhibitor Ventana #760-4840 1X Plus Automation Amplification Diluent Akoya #FP1609 ProLongTM Gold Antifade Mountant Invitrogen #P36930 Mayer’s hemalum solution Sigma-Aldrich 109249 Critical commercial assays Gene imaging kit Vizgen 10400006 Cell Boundary Staining Vizgen 10400118 Merscope FFPE Sample Preparation reagents Vizgen 10400114 Merscope FFPE Slide Vizgen 10500102 1x Automation Amplification Diluent Akoya FP1609 Opal 480 Reagent Pack Akoya FP1500001KT Opal 520 Reagent Pack Akoya FP1487001KT Opal 570 Reagent Pack Akoya FP1488001KT Opal 620 Reagent Pack Akoya FP1495001KT Opal 690 Reagent Pack Akoya FP1497001KT (Continued on next page) Cell Reports Methods 6, 101419, June 15, 2026 e2 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS
Imaging:Article Title: High-throughput histopathology for complex in vitro models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER CytoOne Multiwell Plates Star-Lab CC7682-7524 10% Formalin Sigma-Aldrich HT501320 SuperFrost Ultra Plus Gold Adhesion slides Fisher Scientific 11976299 TeloCol-6 Advanced BioMatrix 5225 Neutralization Solution For TeloCol-6 Advanced BioMatrix 5229 Collagen Rat Tail Type 1 Advanced BioMatrix 5153-1KIT Tris-EDTA buffer, pH 7.8 Ventana #950-227 Discovery Inhibitor Ventana #760-4840 Discovery Ab diluent Ventana #760-108 OmniMap anti-Rabbit HRP Ventana #760-4311 OmniMap anti-Mouse HRP Ventana #760-4310 OmniMap anti-Rat HRP Ventana #760-4457 Discovery ChromoMap DAB Kit Ventana #760-159 Hematoxylin II Ventana #790-2208 Bluing Reagent Ventana #760-2037 Alcohol Roche #CAS64-17-5 Xylol ACROS Organics #444240050 Standard histoglue Pertex #00811-EX DISCOVERY Ab Diluent Ventana 760–108 DISCOVERY Inhibitor Ventana 760–4840 DISCOVERY Goat Ig Block Ventana 760–6008 OmniMap anti-Ms HRP Ventana 760–4310 OmniMap anti-Rb HRP Ventana 760–4311 OmniMap anti-Goat HRP Ventana 760–4647 OmniMap anti-Rat HRP Ventana 760–4457 QD DAPI Ventana 760–4196 ULTRA LCS Ventana 650–210 Discovery CC1 Ventana 950–500 ULTRA LCS Buffer Ventana 950–223 Reaction Buffer Concentrate (10X) Ventana 950–300 DISCOVERY Wash Ventana 950–510 Tris-EDTA buffer pH 7.8 (CC1) Ventana #950-227 Discovery Inhibitor Ventana #760-4840 1X Plus Automation Amplification Diluent Akoya #FP1609 ProLongTM Gold Antifade Mountant Invitrogen #P36930 Mayer’s hemalum solution Sigma-Aldrich 109249 Critical commercial assays Gene imaging kit Vizgen 10400006 Cell Boundary Staining Vizgen 10400118 Merscope FFPE Sample Preparation reagents Vizgen 10400114 Merscope FFPE Slide Vizgen 10500102 1x Automation Amplification Diluent Akoya FP1609 Opal 480 Reagent Pack Akoya FP1500001KT Opal 520 Reagent Pack Akoya FP1487001KT Opal 570 Reagent Pack Akoya FP1488001KT Opal 620 Reagent Pack Akoya FP1495001KT Opal 690 Reagent Pack Akoya FP1497001KT (Continued on next page) Cell Reports Methods 6, 101419, June 15, 2026 e2 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS
Staining:Article Title: High-throughput histopathology for complex in vitro models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER CytoOne Multiwell Plates Star-Lab CC7682-7524 10% Formalin Sigma-Aldrich HT501320 SuperFrost Ultra Plus Gold Adhesion slides Fisher Scientific 11976299 TeloCol-6 Advanced BioMatrix 5225 Neutralization Solution For TeloCol-6 Advanced BioMatrix 5229 Collagen Rat Tail Type 1 Advanced BioMatrix 5153-1KIT Tris-EDTA buffer, pH 7.8 Ventana #950-227 Discovery Inhibitor Ventana #760-4840 Discovery Ab diluent Ventana #760-108 OmniMap anti-Rabbit HRP Ventana #760-4311 OmniMap anti-Mouse HRP Ventana #760-4310 OmniMap anti-Rat HRP Ventana #760-4457 Discovery ChromoMap DAB Kit Ventana #760-159 Hematoxylin II Ventana #790-2208 Bluing Reagent Ventana #760-2037 Alcohol Roche #CAS64-17-5 Xylol ACROS Organics #444240050 Standard histoglue Pertex #00811-EX DISCOVERY Ab Diluent Ventana 760–108 DISCOVERY Inhibitor Ventana 760–4840 DISCOVERY Goat Ig Block Ventana 760–6008 OmniMap anti-Ms HRP Ventana 760–4310 OmniMap anti-Rb HRP Ventana 760–4311 OmniMap anti-Goat HRP Ventana 760–4647 OmniMap anti-Rat HRP Ventana 760–4457 QD DAPI Ventana 760–4196 ULTRA LCS Ventana 650–210 Discovery CC1 Ventana 950–500 ULTRA LCS Buffer Ventana 950–223 Reaction Buffer Concentrate (10X) Ventana 950–300 DISCOVERY Wash Ventana 950–510 Tris-EDTA buffer pH 7.8 (CC1) Ventana #950-227 Discovery Inhibitor Ventana #760-4840 1X Plus Automation Amplification Diluent Akoya #FP1609 ProLongTM Gold Antifade Mountant Invitrogen #P36930 Mayer’s hemalum solution Sigma-Aldrich 109249 Critical commercial assays Gene imaging kit Vizgen 10400006 Cell Boundary Staining Vizgen 10400118 Merscope FFPE Sample Preparation reagents Vizgen 10400114 Merscope FFPE Slide Vizgen 10500102 1x Automation Amplification Diluent Akoya FP1609 Opal 480 Reagent Pack Akoya FP1500001KT Opal 520 Reagent Pack Akoya FP1487001KT Opal 570 Reagent Pack Akoya FP1488001KT Opal 620 Reagent Pack Akoya FP1495001KT Opal 690 Reagent Pack Akoya FP1497001KT (Continued on next page) Cell Reports Methods 6, 101419, June 15, 2026 e2 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS
Formalin-fixed Paraffin-Embedded:Article Title: High-throughput histopathology for complex in vitro models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER CytoOne Multiwell Plates Star-Lab CC7682-7524 10% Formalin Sigma-Aldrich HT501320 SuperFrost Ultra Plus Gold Adhesion slides Fisher Scientific 11976299 TeloCol-6 Advanced BioMatrix 5225 Neutralization Solution For TeloCol-6 Advanced BioMatrix 5229 Collagen Rat Tail Type 1 Advanced BioMatrix 5153-1KIT Tris-EDTA buffer, pH 7.8 Ventana #950-227 Discovery Inhibitor Ventana #760-4840 Discovery Ab diluent Ventana #760-108 OmniMap anti-Rabbit HRP Ventana #760-4311 OmniMap anti-Mouse HRP Ventana #760-4310 OmniMap anti-Rat HRP Ventana #760-4457 Discovery ChromoMap DAB Kit Ventana #760-159 Hematoxylin II Ventana #790-2208 Bluing Reagent Ventana #760-2037 Alcohol Roche #CAS64-17-5 Xylol ACROS Organics #444240050 Standard histoglue Pertex #00811-EX DISCOVERY Ab Diluent Ventana 760–108 DISCOVERY Inhibitor Ventana 760–4840 DISCOVERY Goat Ig Block Ventana 760–6008 OmniMap anti-Ms HRP Ventana 760–4310 OmniMap anti-Rb HRP Ventana 760–4311 OmniMap anti-Goat HRP Ventana 760–4647 OmniMap anti-Rat HRP Ventana 760–4457 QD DAPI Ventana 760–4196 ULTRA LCS Ventana 650–210 Discovery CC1 Ventana 950–500 ULTRA LCS Buffer Ventana 950–223 Reaction Buffer Concentrate (10X) Ventana 950–300 DISCOVERY Wash Ventana 950–510 Tris-EDTA buffer pH 7.8 (CC1) Ventana #950-227 Discovery Inhibitor Ventana #760-4840 1X Plus Automation Amplification Diluent Akoya #FP1609 ProLongTM Gold Antifade Mountant Invitrogen #P36930 Mayer’s hemalum solution Sigma-Aldrich 109249 Critical commercial assays Gene imaging kit Vizgen 10400006 Cell Boundary Staining Vizgen 10400118 Merscope FFPE Sample Preparation reagents Vizgen 10400114 Merscope FFPE Slide Vizgen 10500102 1x Automation Amplification Diluent Akoya FP1609 Opal 480 Reagent Pack Akoya FP1500001KT Opal 520 Reagent Pack Akoya FP1487001KT Opal 570 Reagent Pack Akoya FP1488001KT Opal 620 Reagent Pack Akoya FP1495001KT Opal 690 Reagent Pack Akoya FP1497001KT (Continued on next page) Cell Reports Methods 6, 101419, June 15, 2026 e2 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS
Sample Prep:Article Title: High-throughput histopathology for complex in vitro models.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER CytoOne Multiwell Plates Star-Lab CC7682-7524 10% Formalin Sigma-Aldrich HT501320 SuperFrost Ultra Plus Gold Adhesion slides Fisher Scientific 11976299 TeloCol-6 Advanced BioMatrix 5225 Neutralization Solution For TeloCol-6 Advanced BioMatrix 5229 Collagen Rat Tail Type 1 Advanced BioMatrix 5153-1KIT Tris-EDTA buffer, pH 7.8 Ventana #950-227 Discovery Inhibitor Ventana #760-4840 Discovery Ab diluent Ventana #760-108 OmniMap anti-Rabbit HRP Ventana #760-4311 OmniMap anti-Mouse HRP Ventana #760-4310 OmniMap anti-Rat HRP Ventana #760-4457 Discovery ChromoMap DAB Kit Ventana #760-159 Hematoxylin II Ventana #790-2208 Bluing Reagent Ventana #760-2037 Alcohol Roche #CAS64-17-5 Xylol ACROS Organics #444240050 Standard histoglue Pertex #00811-EX DISCOVERY Ab Diluent Ventana 760–108 DISCOVERY Inhibitor Ventana 760–4840 DISCOVERY Goat Ig Block Ventana 760–6008 OmniMap anti-Ms HRP Ventana 760–4310 OmniMap anti-Rb HRP Ventana 760–4311 OmniMap anti-Goat HRP Ventana 760–4647 OmniMap anti-Rat HRP Ventana 760–4457 QD DAPI Ventana 760–4196 ULTRA LCS Ventana 650–210 Discovery CC1 Ventana 950–500 ULTRA LCS Buffer Ventana 950–223 Reaction Buffer Concentrate (10X) Ventana 950–300 DISCOVERY Wash Ventana 950–510 Tris-EDTA buffer pH 7.8 (CC1) Ventana #950-227 Discovery Inhibitor Ventana #760-4840 1X Plus Automation Amplification Diluent Akoya #FP1609 ProLongTM Gold Antifade Mountant Invitrogen #P36930 Mayer’s hemalum solution Sigma-Aldrich 109249 Critical commercial assays Gene imaging kit Vizgen 10400006 Cell Boundary Staining Vizgen 10400118 Merscope FFPE Sample Preparation reagents Vizgen 10400114 Merscope FFPE Slide Vizgen 10500102 1x Automation Amplification Diluent Akoya FP1609 Opal 480 Reagent Pack Akoya FP1500001KT Opal 520 Reagent Pack Akoya FP1487001KT Opal 570 Reagent Pack Akoya FP1488001KT Opal 620 Reagent Pack Akoya FP1495001KT Opal 690 Reagent Pack Akoya FP1497001KT (Continued on next page) Cell Reports Methods 6, 101419, June 15, 2026 e2 Report ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Recombinant SOX9 (1:800) Abcam Ab185966; RRID: AB_2728660 FABP1 (1:100) Life Technologies PA5-28945; RRID: AB_2546421 MUC2 (1:100) Life Technologies MA5-12345; RRID: AB_10975230 Ki67 (1:500) Invitrogen 14-5698-82; RRID: AB_10854564 CD3 (prediluted) Ventana 790-4341; RRID: AB_2335978 CD4 (prediluted) Ventana 790-4423; RRID: AB_2335982 CD8 (prediluted) Ventana 790-4460; RRID: AB_2335985 CD14 (1:200) Abcam ab181470, RRID:AB_2725781 CD20 (1:200) DAKO M0755 Recombinant CD103 (1:100) Abcam Ab227697; RRID: AB_3665840 Cleaved Caspase-3 (1:100) Cell Signaling Technology 9661; RRID: AB_2341188 EpCAM (prediluted) Ventana 760–4383 E-Cadherin (prediluted) Ventana 760–4497 Granzyme B (1:100) Abcam Ab4059; RRID: AB_304251 Vimentin (prediluted) Ventana 790–2917 CD69 (1:100) Abcam ab233396; RRID: AB_2922929 MUC5AC (1:100) Invitrogen MA5-12178; RRID: AB_10978001 FOXJ1 (1:100) Invitrogen 14-9965-82; RRID: AB_1548835 aTubulin (1:100) Abcam ab218591 PAX6 (1:50) DSHB N/A Rhodopsin (1:200) Abcam Ab5417; RRID: AB_304874 OTX2 (1:200) Atlas/Sigma HPA000633; RRID: AB_1079538 CRX (1:200) Abnova H00001406-M02; RRID: AB_606098 ZO-1 (1:100) Invitrogen 33-9100; RRID: AB_2533147 CD31 (1:100) Dako M0823 CD45 (prediluted) Ventana 760-2505; RRID: AB_2335953 CEACAM5 (1:200) Abcam ab207718; RRID: AB_3086740 Biological samples Human intestinal tissue FFPE blocks Foundation HTCR, Munich, Germany HTCR ethics commission approval: no. 025-12 Human intestinal tissue FFPE blocks Clarunis Basel, Switzerland Ethics Committee of Basel; EKBB, no. 2019-02118 Human intestinal tissue FFPE blocks Humanitas Research Hospital (Milan, Italy) ethics commission Comitato Etico Terrirotiale Lombardia 5 (Ethical approval 3631) Chemicals, peptides, and recombinant proteins Phosphate-Buffered Saline (PBS) Gibco 10010–056 Paraformaldehyde (PFA) Thermo Scientific Chemicals J19943.K2 Advanced DMEM/F12 Thermo Fischer Scientific 12634028 Bovine Serum Albumin (BSA) Sigma-Aldrich A8412 Cell Recovery Solution Corning 354253 Sodium Azide Sigma-Aldrich S2002 Histogel Fisher Scientific 12006679 Puncher of various sizes pfm medical 48401 (Continued on next page) e1 Cell Reports Methods 6, 101419, June 15, 2026 Report ll OPEN ACCESS
|
