Isolation:Article Title: Prospective Breast Cancer Biobanking Project
Article Snippet: .. MiRNA and mRNA will be profiled using PureLinkTM miRNA Isolation Kit (Invitrogen), Dynabeads mRNA direct micro kit (Ambion),) and Ion total RNA-seq kit V2 (Life Technologies) on our Ion Proton NGS instrument. ..
RNA Sequencing:Article Title: Prospective Breast Cancer Biobanking Project
Article Snippet: .. MiRNA and mRNA will be profiled using PureLinkTM miRNA Isolation Kit (Invitrogen), Dynabeads mRNA direct micro kit (Ambion),) and Ion total RNA-seq kit V2 (Life Technologies) on our Ion Proton NGS instrument. ..
Article Title: Compositions and methods for treating breast cancer
Article Snippet: .. Gyorffy 234 Microarray Recurrence-free 68 Breast Cancer Research and (Affymetrix HGU133A survival Treatment 123.3 (2010): 725-731 and HGU133 + 2) METABRIC 269 Microarray Overall survival 110 Nature 486.7403 (2012): 346. (Illumina HT-12 v3) GSE21653 67 Microarray Recurrence-free 52 Breast Cancer Res Treat 2011 (Affymetrix HGU133 Plus 2.0) survival April; 126(2): 407-20 E-MTAB-365 51 Microarray Recurrence-free 51 Bioinformatics 29(9): 1149 (2013) (Affymetrix HGU133 Plus 2.0) survival *only include samples with PAM50 classification as Basal TABLE 10 Survival Status of Low- and High-risk Patient Groups Stratified by Biomarker Gene Sets Number Number Lower Upper of Low- of High- limit of limit of risk risk 5-year Hazard hazard hazard Gene-set group group survival ratio ratio ratio P value TCGA BRAVO_DX 75 50 0.946/0.619* 6.79 1.89 24.37 0.0007 BRAVO_IMMUNE 93 32 0.932/0.43* 7.50 2.50 22.49 <0.0001 GEO BRAVO_DX 161 73 0.665/0.178 3.45 2.41 4.93 <0.0001 BRAVO_IMMUNE 158 76 0.684/0.158 4.33 3.02 6.20 <0.0001 METABRIC BRAVO_DX 103 166 0.771/0.621 1.70 1.16 2.49 0.0055 BRAVO_IMMUNE 155 114 0.731/0.606 1.46 1.03 2.06 0.0332 METABRIC BRAVO_DX 100 137 0.827/0.628 1.91 1.26 2.88 0.0018 (NPI <5.4, BRAVO_IMMUNE 136 101 0.784/0.615 1.69 1.15 2.49 0.0064 low-grade) TABLE 11 Probes of Customized TaqMan Real-Time PCR Assay Correlation with Gene Probe* FPKM from RNA-seq AFAP1L1 Hs00827027_m1 0.9858 AIM2 Hs00915710_m1 0.983 AIM2 Hs00175457_m1 0.9692 ATP6AP1L Hs01372641_m1 0.9491 ATP6AP1L Hs01372640_m1 0.8393 CLEC4E Hs00372017_m1 0.8359 DNAJC1 Hs01550854_m1 0.9103 DNAJC1 Hs01550849_m1 0.8903 ELF3 Hs00963881_m1 0.986 ELF3 Hs00231786_m1 0.9825 EPHB4 Hs01119118_g1 0.9422 EPHB4 Hs00174752_m1 0.8286 FGF1 Hs00265254_m1 0.8547 FGF1 Hs01092738_m1 0.738 FKBP5 Hs01561003_m1 0.976 FKBP5 Hs01561006_m1 0.9585 GLIS1 Hs00377690_m1 0.925 HAVCR1 Hs00930379_g1 0.8137 HAVCR1 Hs00273334_m1 below detection limit IKZF3 Hs00232635_m1 0.9881 IKZF3 Hs00918017_m1 0.978 ING4 Hs00211773_m1 0.8782 ING4 Hs01088027_g1 0.7332 LMTK2 Hs00905745_m1 0.7828 LMTK2 Hs00208698_m1 0.6208 MKRN2 Hs00274055_m1 0.8412 MREG Hs00215942_m1 0.9422 MREG Hs01066515_m1 0.8877 NCR1 Hs00950809_g1 0.9483 NCR1 Hs00183118_m1 0.9179 PCYT1A Hs00192339_m1 0.9098 PCYT1A Hs02564656_s1 0.9079 RGL2 Hs00191084_m1 0.8906 SLAMF6 Hs00372941_m1 0.9488 SLAMF6 Hs01559920_m1 0.9382 TMEM30A Hs01092148_m1 0.8262 TMEM30A Hs01097969_ml 0.3723 EIF2B1 Hs00426752_m1 NA CASC3 Hs00201226_m1 NA HMBS Hs00609296_g1 NA POP4 Hs00198357_m1 NA Casc3 Mm01296308_m1 NA Hmbs Mm01143545_m1 NA ..
Next-Generation Sequencing:Article Title: Prospective Breast Cancer Biobanking Project
Article Snippet: .. MiRNA and mRNA will be profiled using PureLinkTM miRNA Isolation Kit (Invitrogen), Dynabeads mRNA direct micro kit (Ambion),) and Ion total RNA-seq kit V2 (Life Technologies) on our Ion Proton NGS instrument. ..
Reverse Transcription:Article Title: Bacterial reporter–paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defense
Article Snippet: HMDM viability was assessed to be >80% by Trypan blue exclusion counted on a Countess TM 3 FL Automated Cell Counter (ThermoFisher). .. Standard reagents (excluding the oligo-dT reverse transcription primer) were prepared for a modified 5’ scRNA-seq 10× Genomics workflow ( SI Appendix , Fig. S2 C , Chromium Single Cell 5’ Reagent Kits User Guide CG000331 [v2 Chemistry Dual Index]), with additional reagents included for the indicated purpose: 333 U ReadyTM Lyse Lysozyme and 0.32 mM Ambion® EDTA, to aid bacterial lysis; 40 μM random hexamer (RH) primer with PCR handle (Integrated DNA Technologies, Iowa) to allow reverse transcription of mammalian and bacterial transcripts; and 30 U Vaccinia capping enzyme (NEB), 1.3× capping buffer (NEB), 0.8 mM GTP (NEB), 0.8 mM SAM (NEB), and 0.004 U yeast pyrophosphatase (NEB), to encourage template switching during reverse transcription of bacterial transcripts. ..
Modification:Article Title: Bacterial reporter–paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defense
Article Snippet: HMDM viability was assessed to be >80% by Trypan blue exclusion counted on a Countess TM 3 FL Automated Cell Counter (ThermoFisher). .. Standard reagents (excluding the oligo-dT reverse transcription primer) were prepared for a modified 5’ scRNA-seq 10× Genomics workflow ( SI Appendix , Fig. S2 C , Chromium Single Cell 5’ Reagent Kits User Guide CG000331 [v2 Chemistry Dual Index]), with additional reagents included for the indicated purpose: 333 U ReadyTM Lyse Lysozyme and 0.32 mM Ambion® EDTA, to aid bacterial lysis; 40 μM random hexamer (RH) primer with PCR handle (Integrated DNA Technologies, Iowa) to allow reverse transcription of mammalian and bacterial transcripts; and 30 U Vaccinia capping enzyme (NEB), 1.3× capping buffer (NEB), 0.8 mM GTP (NEB), 0.8 mM SAM (NEB), and 0.004 U yeast pyrophosphatase (NEB), to encourage template switching during reverse transcription of bacterial transcripts. ..
Single Cell:Article Title: Bacterial reporter–paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defense
Article Snippet: HMDM viability was assessed to be >80% by Trypan blue exclusion counted on a Countess TM 3 FL Automated Cell Counter (ThermoFisher). .. Standard reagents (excluding the oligo-dT reverse transcription primer) were prepared for a modified 5’ scRNA-seq 10× Genomics workflow ( SI Appendix , Fig. S2 C , Chromium Single Cell 5’ Reagent Kits User Guide CG000331 [v2 Chemistry Dual Index]), with additional reagents included for the indicated purpose: 333 U ReadyTM Lyse Lysozyme and 0.32 mM Ambion® EDTA, to aid bacterial lysis; 40 μM random hexamer (RH) primer with PCR handle (Integrated DNA Technologies, Iowa) to allow reverse transcription of mammalian and bacterial transcripts; and 30 U Vaccinia capping enzyme (NEB), 1.3× capping buffer (NEB), 0.8 mM GTP (NEB), 0.8 mM SAM (NEB), and 0.004 U yeast pyrophosphatase (NEB), to encourage template switching during reverse transcription of bacterial transcripts. ..
Article Title: Single-cell Transcriptomics Reveal Altered B cell Responses and T cell Senescence in Geriatric Non-responders to COVID-19 mRNA Vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Human Phycoerythrin-conjugated Donkey F(ab)2 IgG, with Fcγ Jackson ImmunoResearch RRID: AB_2340519 Human monoclonal HLA-DR FITC Biolegend RRID: AB_314682 Human monoclonal CD19 APC eBioscience RRID: AB_10804519 Human monoclonal CD38 Alexa Fluor 700 Biolegend RRID: AB_2072781 Human monoclonal CD14 APC-Cy7 Biolegend RRID: AB_830693 Human monoclonal CD56 Pacific Blue Biolegend RRID: AB_10612566 Human monoclonal CD25 BV605 Biolegend RRID: AB_11218989 Human monoclonal CD8 BV786 BD RRID: AB_2687487 Human monoclonal PD-1 PE-Cy-7 Biolegend RRID: AB_2159324 Human monoclonal CD3 BUV395 BD RRID: AB_2744387 Human monoclonal CD45RA PE Texas Red Invitrogen RRID: AB_10372222 Human monoclonal CD74 BUV805 Biolegend RRID: AB_2075505 Human monoclonal CD4 BUV805 BD RRID: AB_2744423 Bacterial and virus strains Stabilized full-length S protein (aa 16-1230 with furin site mutated) Canaday et al., 2021 N/A SARS-CoV-2 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 D614G pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Phosphate-Buffered Saline (DPBS) Invitrogen Cat # 14190144 Bovine Serum Albumin (BSA) Invitrogen Cat # AM2616 RPMI (1640) Medium Corning Cat # 10-040-CV Fetal Bovine Serum Gibco Cat # 10438026 DMSO Sigma Cat # D2650-100ML Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3.1 10X Genomics Cat # 1000121 Chromium Next GEM Chip G Single Cell 10X Genomics Cat # 10001210 Single Index Kit N, Set A 10X Genomics Cat # 1000212 Live Dead Fixable Aqua Viability Kit Invitrogen Cat# NC0180395 Deposited data Processed single cell RNA-seq data Gene Expression Omnibus GSE300265 Software and algorithms Cellranger v4.0.0 10X Genomics RRID:SCR_0173 R (programming language) v4.1.1 R RRID:SCR_001905 Seurat R package v4.1.1 Hao et al. 2021 RRID:SCR_016341 Harmony R package v0.1.0 Broad Institute RRID:SCR_022206 ggplot2 R package R RRID:SCR_014601 BioRender BioRender RRID:SCR_018361 Gene Set Enrichment algorithm (GSEA) Broad Institute RRID:SCR_003199 Cytoscape v3.10.3 Cytoscape Consortium RRID:SCR_003032 Drug Perturbation Enrichment algorithm (dpGSEA) Fang et al., 2021 RRID:SCR_025351 Limma package (Bioconducter) Ritchie et al., 2015 RRID:SCR_010943 Python v3.9.7 Python RRID:SCR_008394 (Continued on next page) e1 iScience 29, 115730, May 15, 2026 ..
Article Title: In vivo evolution of antibody CR3022 expands cross-neutralization of SARS-CoV-2 variants and informs pan-sarbecovirus immunity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Sigma Adjuvant System (Ribi) Sigma Cat#S6322 LIVE/DEADTM Fixable Blue Dead Cell Stain Kit ThermoFisher Scientific Cat#L23105 7-AAD Biolegend Cat#420404 Buffer TCL 2X QIAGEN Cat#1070498 SuperScriptTM IV First-Strand Synthesis System ThermoFisher Scientific Cat#18091050 NextSeqTM1000/2000 P1/2 Reagents (300 cycles) Illumina Cat#20050264/20046812 SARS-CoV spike (6P) This manuscript N/A SARS-CoV-2 spike (6P) This manuscript N/A SARS-CoV RBD This manuscript N/A SARS-CoV-2 RBD This manuscript N/A Banal-52 RBD This manuscript N/A Alt-RTM S.p. .. Cas9 Nuclease V3 IDT Cat#1081058 EZ-Link sulfo-NHS-Biotin ThermoFisher Scientific Cat#A39256 Protein A resin GenScript Cat#L00210-50 Ni-NTA agarose beads Qiagen Cat#30230 Aquablue ELISA substrate ThermoFisher Scientific Cat#00-4203-58 Ophenylenediamine dihydrochloride (OPD) Sigma Cat#P9187-50SET Streptavidin-HRP Southern Biotech Cat#7105-05 Critical commercial assays Steady-Glo® Luciferase Assay System Promega Cat#E2550 Chromium Next GEM Single Cell 5′ Kit v2 10X Genomics Cat#1000263 Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat#1000286 Chromium Single Cell 5′ Feature Barcode Kit 10X Genomics Cat#1000256 Chromium Single Cell Mouse BCR Amplification Kit 10X Genomics Cat#1000255 Chromium Single cell Library Construction Kit 10X Genomics Cat#1000352 Deposited data Single cell RNA-seq datasets This manuscript GEO: GSE304367 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3 This manuscript PDB: 9PSN Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-622 and CC12.3 This manuscript PDB: 9PSO Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3 This manuscript PDB: 9PSP Experimental models: Cell lines Expi293F cells ThermoFisher Scientific Cat#14635 Vero E6 cells BEI Resources Cat#NR-54970 Sf9 cells ATCC Cat#CRL-1711; RRID: CVCL_0549 High Five cells Thermo Fisher Scientific Cat#B85502; RRID: CVCL_C190 Experimental models: Organisms/strains glCR3022H transgenic mouse This manuscript N/A C57BL/6 mouse Jackson lab Cat#000664 B6.SJL-Ptprca Pepcb/BoyJ Jackson lab Cat#002014 Oligonucleotides crRNA:tracrRNA IDT Cat#1072534 Mouse single-cell PCR primer sets von Boehmer et al.43 N/A (Continued on next page) 18 Cell Reports 45, 117137, April 28, 2026 .. Expi293F cells were maintained in Expi293 Expression Medium (Thermo Scientific) at 37◦C in a shaking incubator supplied with 8% CO2.
Article Title: Engineered intestinal crypt geometry uncovers YAP1-dependent fetal-to-adult transition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-E-Cadherin Clone 36/E-Cadherin (RUO) BD Bioscience 610181; RRID: AB_397580 CD44var (v6) Monoclonal Antibody (9A4) Invitrogen BMS145; RRID: AB_10597738 Lysozyme 1(EC.3.2.1.17) DAKO A0099; RRID: AB_2341231 EpCAM (Clone G8.8) ThermoFisher #17-5791-82; RRID: AB_2716944 BD PharmingenTM PE-CyTM7 Rat Anti-Mouse CD45 BD Bioscience 552848; RRID: AB_394489 CD31 (PECAM-1) Monoclonal Antibody (390), PE-Cyanine7 ThermoFisher 25-0311-82; RRID: AB_2869771 Keratin K20 Nordic Biosite/Progen 318-GP-K20; RRID: AB_1541036 YAP (D8H1X) Cell Signaling #14074; RRID: AB_2650491 Alexa Flour 488 Donkey anti Rabbit IgG (H+L) ThermoFisher A-21206 Alexa Fluor 488 Donkey anti Rat IgG (H+L) ThermoFisher A-21208 Alexa Fluor 555 Goat anti mouse IgG2a ThermoFisher A21137 Chemicals, peptides, and recombinant proteins 4-hydroxytamoxifen Sigma-Aldrich H6278 RapiClear 1.52 Sunjin Lab RC152002 Y-27632 dihydrochloride Sigma-Aldrich Y0503 N-Acetyl-L-cysteine Sigma-Aldrich A9165 Next-Generation Surrogate Wnt K. Christopher Garcia Miao et al. 55 Human EGF Peprotech AF-100-15 Murine Noggin Peprotech 250–38 R-spondin 1 conditioned medium in-house production N/A N2 Gibco 17502048 B27 Gibco 12587010 Diphtheria Toxin Merck D0564 Doxycycline hyclate Sigma-Aldrich D9891 Critical commercial assays TotalSeq hashtag antibodies Biolegend A0301, A0302, A0303, and A0304 Rneasy Micro Kit Qiagen 74004 Chromium Next GEM Single Cell 3 ′ Kit v3.1 10× Genomics PN-1000263 Library Construction Kit, 16 rxns 10× Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10× Genomics PN-1000287 Dual Index Kit TT Set A 10× Genomics PN-1000215 RNAscope Multiplex Fluorescent Reagent Kit v2 ACD Biotechne 323100 RNAscope probe mm-Atoh1 ACD Biotechne 408791-C3 RNAscope probe mm-Lyz1 ACD Biotechne 415131 Deposited data Single cell RNA-seq data This study GSE247255 scRNA-seq dataset from adult intestinal epithelium Haber et al. 29 GSE92332 scRNA-seq dataset from adult organoids Hansen et al. 32 GSE221278 scRNA-seq dataset from fetal progenitors Hansen et al. 32 GSE221278 Segmentation dataset and model This study https://zenodo.org/records/17565548 Experimental models: Organisms/strains C57BL/6J Taconic 17758-F Top.CFP Palle Serup Serup et al. 56 (Continued on next page) e1 Cell Stem Cell 33, 1–15.e1–e7, March 5, 2026 ..
Lysis:Article Title: Bacterial reporter–paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defense
Article Snippet: HMDM viability was assessed to be >80% by Trypan blue exclusion counted on a Countess TM 3 FL Automated Cell Counter (ThermoFisher). .. Standard reagents (excluding the oligo-dT reverse transcription primer) were prepared for a modified 5’ scRNA-seq 10× Genomics workflow ( SI Appendix , Fig. S2 C , Chromium Single Cell 5’ Reagent Kits User Guide CG000331 [v2 Chemistry Dual Index]), with additional reagents included for the indicated purpose: 333 U ReadyTM Lyse Lysozyme and 0.32 mM Ambion® EDTA, to aid bacterial lysis; 40 μM random hexamer (RH) primer with PCR handle (Integrated DNA Technologies, Iowa) to allow reverse transcription of mammalian and bacterial transcripts; and 30 U Vaccinia capping enzyme (NEB), 1.3× capping buffer (NEB), 0.8 mM GTP (NEB), 0.8 mM SAM (NEB), and 0.004 U yeast pyrophosphatase (NEB), to encourage template switching during reverse transcription of bacterial transcripts. ..
Random Hexamer:Article Title: Bacterial reporter–paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defense
Article Snippet: HMDM viability was assessed to be >80% by Trypan blue exclusion counted on a Countess TM 3 FL Automated Cell Counter (ThermoFisher). .. Standard reagents (excluding the oligo-dT reverse transcription primer) were prepared for a modified 5’ scRNA-seq 10× Genomics workflow ( SI Appendix , Fig. S2 C , Chromium Single Cell 5’ Reagent Kits User Guide CG000331 [v2 Chemistry Dual Index]), with additional reagents included for the indicated purpose: 333 U ReadyTM Lyse Lysozyme and 0.32 mM Ambion® EDTA, to aid bacterial lysis; 40 μM random hexamer (RH) primer with PCR handle (Integrated DNA Technologies, Iowa) to allow reverse transcription of mammalian and bacterial transcripts; and 30 U Vaccinia capping enzyme (NEB), 1.3× capping buffer (NEB), 0.8 mM GTP (NEB), 0.8 mM SAM (NEB), and 0.004 U yeast pyrophosphatase (NEB), to encourage template switching during reverse transcription of bacterial transcripts. ..
Polymerase Chain Reaction:Article Title: Bacterial reporter–paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defense
Article Snippet: HMDM viability was assessed to be >80% by Trypan blue exclusion counted on a Countess TM 3 FL Automated Cell Counter (ThermoFisher). .. Standard reagents (excluding the oligo-dT reverse transcription primer) were prepared for a modified 5’ scRNA-seq 10× Genomics workflow ( SI Appendix , Fig. S2 C , Chromium Single Cell 5’ Reagent Kits User Guide CG000331 [v2 Chemistry Dual Index]), with additional reagents included for the indicated purpose: 333 U ReadyTM Lyse Lysozyme and 0.32 mM Ambion® EDTA, to aid bacterial lysis; 40 μM random hexamer (RH) primer with PCR handle (Integrated DNA Technologies, Iowa) to allow reverse transcription of mammalian and bacterial transcripts; and 30 U Vaccinia capping enzyme (NEB), 1.3× capping buffer (NEB), 0.8 mM GTP (NEB), 0.8 mM SAM (NEB), and 0.004 U yeast pyrophosphatase (NEB), to encourage template switching during reverse transcription of bacterial transcripts. ..
Article Title: In vivo evolution of antibody CR3022 expands cross-neutralization of SARS-CoV-2 variants and informs pan-sarbecovirus immunity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Sigma Adjuvant System (Ribi) Sigma Cat#S6322 LIVE/DEADTM Fixable Blue Dead Cell Stain Kit ThermoFisher Scientific Cat#L23105 7-AAD Biolegend Cat#420404 Buffer TCL 2X QIAGEN Cat#1070498 SuperScriptTM IV First-Strand Synthesis System ThermoFisher Scientific Cat#18091050 NextSeqTM1000/2000 P1/2 Reagents (300 cycles) Illumina Cat#20050264/20046812 SARS-CoV spike (6P) This manuscript N/A SARS-CoV-2 spike (6P) This manuscript N/A SARS-CoV RBD This manuscript N/A SARS-CoV-2 RBD This manuscript N/A Banal-52 RBD This manuscript N/A Alt-RTM S.p. .. Cas9 Nuclease V3 IDT Cat#1081058 EZ-Link sulfo-NHS-Biotin ThermoFisher Scientific Cat#A39256 Protein A resin GenScript Cat#L00210-50 Ni-NTA agarose beads Qiagen Cat#30230 Aquablue ELISA substrate ThermoFisher Scientific Cat#00-4203-58 Ophenylenediamine dihydrochloride (OPD) Sigma Cat#P9187-50SET Streptavidin-HRP Southern Biotech Cat#7105-05 Critical commercial assays Steady-Glo® Luciferase Assay System Promega Cat#E2550 Chromium Next GEM Single Cell 5′ Kit v2 10X Genomics Cat#1000263 Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat#1000286 Chromium Single Cell 5′ Feature Barcode Kit 10X Genomics Cat#1000256 Chromium Single Cell Mouse BCR Amplification Kit 10X Genomics Cat#1000255 Chromium Single cell Library Construction Kit 10X Genomics Cat#1000352 Deposited data Single cell RNA-seq datasets This manuscript GEO: GSE304367 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3 This manuscript PDB: 9PSN Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-622 and CC12.3 This manuscript PDB: 9PSO Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3 This manuscript PDB: 9PSP Experimental models: Cell lines Expi293F cells ThermoFisher Scientific Cat#14635 Vero E6 cells BEI Resources Cat#NR-54970 Sf9 cells ATCC Cat#CRL-1711; RRID: CVCL_0549 High Five cells Thermo Fisher Scientific Cat#B85502; RRID: CVCL_C190 Experimental models: Organisms/strains glCR3022H transgenic mouse This manuscript N/A C57BL/6 mouse Jackson lab Cat#000664 B6.SJL-Ptprca Pepcb/BoyJ Jackson lab Cat#002014 Oligonucleotides crRNA:tracrRNA IDT Cat#1072534 Mouse single-cell PCR primer sets von Boehmer et al.43 N/A (Continued on next page) 18 Cell Reports 45, 117137, April 28, 2026 .. Expi293F cells were maintained in Expi293 Expression Medium (Thermo Scientific) at 37◦C in a shaking incubator supplied with 8% CO2.
Microscopy:Article Title: Altered chromatin accessibility and nucleosome positioning landscape upon HDAC and LSD1 inhibition in cancer cell
Article Snippet: 3 μl of RNAse A (NEB # T3018L) was also added to the labeling reaction and incubated at 37 °C for 30 min to digest cellular RNA. .. Slides were washed once with NEED-seq washing buffer (20 mM phosphate buffer, 0.5 M NaCl, and 1 % Triton X-100) and were air dried, mounted using Prolong Gold antifade reagent with DAPI (Invitrogen, P36935) and visualized using LSM 880 confocal microscope (Zeiss). ..
Microarray:Article Title: Compositions and methods for treating breast cancer
Article Snippet: .. Gyorffy 234 Microarray Recurrence-free 68 Breast Cancer Research and (Affymetrix HGU133A survival Treatment 123.3 (2010): 725-731 and HGU133 + 2) METABRIC 269 Microarray Overall survival 110 Nature 486.7403 (2012): 346. (Illumina HT-12 v3) GSE21653 67 Microarray Recurrence-free 52 Breast Cancer Res Treat 2011 (Affymetrix HGU133 Plus 2.0) survival April; 126(2): 407-20 E-MTAB-365 51 Microarray Recurrence-free 51 Bioinformatics 29(9): 1149 (2013) (Affymetrix HGU133 Plus 2.0) survival *only include samples with PAM50 classification as Basal TABLE 10 Survival Status of Low- and High-risk Patient Groups Stratified by Biomarker Gene Sets Number Number Lower Upper of Low- of High- limit of limit of risk risk 5-year Hazard hazard hazard Gene-set group group survival ratio ratio ratio P value TCGA BRAVO_DX 75 50 0.946/0.619* 6.79 1.89 24.37 0.0007 BRAVO_IMMUNE 93 32 0.932/0.43* 7.50 2.50 22.49 <0.0001 GEO BRAVO_DX 161 73 0.665/0.178 3.45 2.41 4.93 <0.0001 BRAVO_IMMUNE 158 76 0.684/0.158 4.33 3.02 6.20 <0.0001 METABRIC BRAVO_DX 103 166 0.771/0.621 1.70 1.16 2.49 0.0055 BRAVO_IMMUNE 155 114 0.731/0.606 1.46 1.03 2.06 0.0332 METABRIC BRAVO_DX 100 137 0.827/0.628 1.91 1.26 2.88 0.0018 (NPI <5.4, BRAVO_IMMUNE 136 101 0.784/0.615 1.69 1.15 2.49 0.0064 low-grade) TABLE 11 Probes of Customized TaqMan Real-Time PCR Assay Correlation with Gene Probe* FPKM from RNA-seq AFAP1L1 Hs00827027_m1 0.9858 AIM2 Hs00915710_m1 0.983 AIM2 Hs00175457_m1 0.9692 ATP6AP1L Hs01372641_m1 0.9491 ATP6AP1L Hs01372640_m1 0.8393 CLEC4E Hs00372017_m1 0.8359 DNAJC1 Hs01550854_m1 0.9103 DNAJC1 Hs01550849_m1 0.8903 ELF3 Hs00963881_m1 0.986 ELF3 Hs00231786_m1 0.9825 EPHB4 Hs01119118_g1 0.9422 EPHB4 Hs00174752_m1 0.8286 FGF1 Hs00265254_m1 0.8547 FGF1 Hs01092738_m1 0.738 FKBP5 Hs01561003_m1 0.976 FKBP5 Hs01561006_m1 0.9585 GLIS1 Hs00377690_m1 0.925 HAVCR1 Hs00930379_g1 0.8137 HAVCR1 Hs00273334_m1 below detection limit IKZF3 Hs00232635_m1 0.9881 IKZF3 Hs00918017_m1 0.978 ING4 Hs00211773_m1 0.8782 ING4 Hs01088027_g1 0.7332 LMTK2 Hs00905745_m1 0.7828 LMTK2 Hs00208698_m1 0.6208 MKRN2 Hs00274055_m1 0.8412 MREG Hs00215942_m1 0.9422 MREG Hs01066515_m1 0.8877 NCR1 Hs00950809_g1 0.9483 NCR1 Hs00183118_m1 0.9179 PCYT1A Hs00192339_m1 0.9098 PCYT1A Hs02564656_s1 0.9079 RGL2 Hs00191084_m1 0.8906 SLAMF6 Hs00372941_m1 0.9488 SLAMF6 Hs01559920_m1 0.9382 TMEM30A Hs01092148_m1 0.8262 TMEM30A Hs01097969_ml 0.3723 EIF2B1 Hs00426752_m1 NA CASC3 Hs00201226_m1 NA HMBS Hs00609296_g1 NA POP4 Hs00198357_m1 NA Casc3 Mm01296308_m1 NA Hmbs Mm01143545_m1 NA ..
Biomarker Discovery:Article Title: Compositions and methods for treating breast cancer
Article Snippet: .. Gyorffy 234 Microarray Recurrence-free 68 Breast Cancer Research and (Affymetrix HGU133A survival Treatment 123.3 (2010): 725-731 and HGU133 + 2) METABRIC 269 Microarray Overall survival 110 Nature 486.7403 (2012): 346. (Illumina HT-12 v3) GSE21653 67 Microarray Recurrence-free 52 Breast Cancer Res Treat 2011 (Affymetrix HGU133 Plus 2.0) survival April; 126(2): 407-20 E-MTAB-365 51 Microarray Recurrence-free 51 Bioinformatics 29(9): 1149 (2013) (Affymetrix HGU133 Plus 2.0) survival *only include samples with PAM50 classification as Basal TABLE 10 Survival Status of Low- and High-risk Patient Groups Stratified by Biomarker Gene Sets Number Number Lower Upper of Low- of High- limit of limit of risk risk 5-year Hazard hazard hazard Gene-set group group survival ratio ratio ratio P value TCGA BRAVO_DX 75 50 0.946/0.619* 6.79 1.89 24.37 0.0007 BRAVO_IMMUNE 93 32 0.932/0.43* 7.50 2.50 22.49 <0.0001 GEO BRAVO_DX 161 73 0.665/0.178 3.45 2.41 4.93 <0.0001 BRAVO_IMMUNE 158 76 0.684/0.158 4.33 3.02 6.20 <0.0001 METABRIC BRAVO_DX 103 166 0.771/0.621 1.70 1.16 2.49 0.0055 BRAVO_IMMUNE 155 114 0.731/0.606 1.46 1.03 2.06 0.0332 METABRIC BRAVO_DX 100 137 0.827/0.628 1.91 1.26 2.88 0.0018 (NPI <5.4, BRAVO_IMMUNE 136 101 0.784/0.615 1.69 1.15 2.49 0.0064 low-grade) TABLE 11 Probes of Customized TaqMan Real-Time PCR Assay Correlation with Gene Probe* FPKM from RNA-seq AFAP1L1 Hs00827027_m1 0.9858 AIM2 Hs00915710_m1 0.983 AIM2 Hs00175457_m1 0.9692 ATP6AP1L Hs01372641_m1 0.9491 ATP6AP1L Hs01372640_m1 0.8393 CLEC4E Hs00372017_m1 0.8359 DNAJC1 Hs01550854_m1 0.9103 DNAJC1 Hs01550849_m1 0.8903 ELF3 Hs00963881_m1 0.986 ELF3 Hs00231786_m1 0.9825 EPHB4 Hs01119118_g1 0.9422 EPHB4 Hs00174752_m1 0.8286 FGF1 Hs00265254_m1 0.8547 FGF1 Hs01092738_m1 0.738 FKBP5 Hs01561003_m1 0.976 FKBP5 Hs01561006_m1 0.9585 GLIS1 Hs00377690_m1 0.925 HAVCR1 Hs00930379_g1 0.8137 HAVCR1 Hs00273334_m1 below detection limit IKZF3 Hs00232635_m1 0.9881 IKZF3 Hs00918017_m1 0.978 ING4 Hs00211773_m1 0.8782 ING4 Hs01088027_g1 0.7332 LMTK2 Hs00905745_m1 0.7828 LMTK2 Hs00208698_m1 0.6208 MKRN2 Hs00274055_m1 0.8412 MREG Hs00215942_m1 0.9422 MREG Hs01066515_m1 0.8877 NCR1 Hs00950809_g1 0.9483 NCR1 Hs00183118_m1 0.9179 PCYT1A Hs00192339_m1 0.9098 PCYT1A Hs02564656_s1 0.9079 RGL2 Hs00191084_m1 0.8906 SLAMF6 Hs00372941_m1 0.9488 SLAMF6 Hs01559920_m1 0.9382 TMEM30A Hs01092148_m1 0.8262 TMEM30A Hs01097969_ml 0.3723 EIF2B1 Hs00426752_m1 NA CASC3 Hs00201226_m1 NA HMBS Hs00609296_g1 NA POP4 Hs00198357_m1 NA Casc3 Mm01296308_m1 NA Hmbs Mm01143545_m1 NA ..
Real-time Polymerase Chain Reaction:Article Title: Compositions and methods for treating breast cancer
Article Snippet: .. Gyorffy 234 Microarray Recurrence-free 68 Breast Cancer Research and (Affymetrix HGU133A survival Treatment 123.3 (2010): 725-731 and HGU133 + 2) METABRIC 269 Microarray Overall survival 110 Nature 486.7403 (2012): 346. (Illumina HT-12 v3) GSE21653 67 Microarray Recurrence-free 52 Breast Cancer Res Treat 2011 (Affymetrix HGU133 Plus 2.0) survival April; 126(2): 407-20 E-MTAB-365 51 Microarray Recurrence-free 51 Bioinformatics 29(9): 1149 (2013) (Affymetrix HGU133 Plus 2.0) survival *only include samples with PAM50 classification as Basal TABLE 10 Survival Status of Low- and High-risk Patient Groups Stratified by Biomarker Gene Sets Number Number Lower Upper of Low- of High- limit of limit of risk risk 5-year Hazard hazard hazard Gene-set group group survival ratio ratio ratio P value TCGA BRAVO_DX 75 50 0.946/0.619* 6.79 1.89 24.37 0.0007 BRAVO_IMMUNE 93 32 0.932/0.43* 7.50 2.50 22.49 <0.0001 GEO BRAVO_DX 161 73 0.665/0.178 3.45 2.41 4.93 <0.0001 BRAVO_IMMUNE 158 76 0.684/0.158 4.33 3.02 6.20 <0.0001 METABRIC BRAVO_DX 103 166 0.771/0.621 1.70 1.16 2.49 0.0055 BRAVO_IMMUNE 155 114 0.731/0.606 1.46 1.03 2.06 0.0332 METABRIC BRAVO_DX 100 137 0.827/0.628 1.91 1.26 2.88 0.0018 (NPI <5.4, BRAVO_IMMUNE 136 101 0.784/0.615 1.69 1.15 2.49 0.0064 low-grade) TABLE 11 Probes of Customized TaqMan Real-Time PCR Assay Correlation with Gene Probe* FPKM from RNA-seq AFAP1L1 Hs00827027_m1 0.9858 AIM2 Hs00915710_m1 0.983 AIM2 Hs00175457_m1 0.9692 ATP6AP1L Hs01372641_m1 0.9491 ATP6AP1L Hs01372640_m1 0.8393 CLEC4E Hs00372017_m1 0.8359 DNAJC1 Hs01550854_m1 0.9103 DNAJC1 Hs01550849_m1 0.8903 ELF3 Hs00963881_m1 0.986 ELF3 Hs00231786_m1 0.9825 EPHB4 Hs01119118_g1 0.9422 EPHB4 Hs00174752_m1 0.8286 FGF1 Hs00265254_m1 0.8547 FGF1 Hs01092738_m1 0.738 FKBP5 Hs01561003_m1 0.976 FKBP5 Hs01561006_m1 0.9585 GLIS1 Hs00377690_m1 0.925 HAVCR1 Hs00930379_g1 0.8137 HAVCR1 Hs00273334_m1 below detection limit IKZF3 Hs00232635_m1 0.9881 IKZF3 Hs00918017_m1 0.978 ING4 Hs00211773_m1 0.8782 ING4 Hs01088027_g1 0.7332 LMTK2 Hs00905745_m1 0.7828 LMTK2 Hs00208698_m1 0.6208 MKRN2 Hs00274055_m1 0.8412 MREG Hs00215942_m1 0.9422 MREG Hs01066515_m1 0.8877 NCR1 Hs00950809_g1 0.9483 NCR1 Hs00183118_m1 0.9179 PCYT1A Hs00192339_m1 0.9098 PCYT1A Hs02564656_s1 0.9079 RGL2 Hs00191084_m1 0.8906 SLAMF6 Hs00372941_m1 0.9488 SLAMF6 Hs01559920_m1 0.9382 TMEM30A Hs01092148_m1 0.8262 TMEM30A Hs01097969_ml 0.3723 EIF2B1 Hs00426752_m1 NA CASC3 Hs00201226_m1 NA HMBS Hs00609296_g1 NA POP4 Hs00198357_m1 NA Casc3 Mm01296308_m1 NA Hmbs Mm01143545_m1 NA ..
Virus:Article Title: Single-cell Transcriptomics Reveal Altered B cell Responses and T cell Senescence in Geriatric Non-responders to COVID-19 mRNA Vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Human Phycoerythrin-conjugated Donkey F(ab)2 IgG, with Fcγ Jackson ImmunoResearch RRID: AB_2340519 Human monoclonal HLA-DR FITC Biolegend RRID: AB_314682 Human monoclonal CD19 APC eBioscience RRID: AB_10804519 Human monoclonal CD38 Alexa Fluor 700 Biolegend RRID: AB_2072781 Human monoclonal CD14 APC-Cy7 Biolegend RRID: AB_830693 Human monoclonal CD56 Pacific Blue Biolegend RRID: AB_10612566 Human monoclonal CD25 BV605 Biolegend RRID: AB_11218989 Human monoclonal CD8 BV786 BD RRID: AB_2687487 Human monoclonal PD-1 PE-Cy-7 Biolegend RRID: AB_2159324 Human monoclonal CD3 BUV395 BD RRID: AB_2744387 Human monoclonal CD45RA PE Texas Red Invitrogen RRID: AB_10372222 Human monoclonal CD74 BUV805 Biolegend RRID: AB_2075505 Human monoclonal CD4 BUV805 BD RRID: AB_2744423 Bacterial and virus strains Stabilized full-length S protein (aa 16-1230 with furin site mutated) Canaday et al., 2021 N/A SARS-CoV-2 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 D614G pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Phosphate-Buffered Saline (DPBS) Invitrogen Cat # 14190144 Bovine Serum Albumin (BSA) Invitrogen Cat # AM2616 RPMI (1640) Medium Corning Cat # 10-040-CV Fetal Bovine Serum Gibco Cat # 10438026 DMSO Sigma Cat # D2650-100ML Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3.1 10X Genomics Cat # 1000121 Chromium Next GEM Chip G Single Cell 10X Genomics Cat # 10001210 Single Index Kit N, Set A 10X Genomics Cat # 1000212 Live Dead Fixable Aqua Viability Kit Invitrogen Cat# NC0180395 Deposited data Processed single cell RNA-seq data Gene Expression Omnibus GSE300265 Software and algorithms Cellranger v4.0.0 10X Genomics RRID:SCR_0173 R (programming language) v4.1.1 R RRID:SCR_001905 Seurat R package v4.1.1 Hao et al. 2021 RRID:SCR_016341 Harmony R package v0.1.0 Broad Institute RRID:SCR_022206 ggplot2 R package R RRID:SCR_014601 BioRender BioRender RRID:SCR_018361 Gene Set Enrichment algorithm (GSEA) Broad Institute RRID:SCR_003199 Cytoscape v3.10.3 Cytoscape Consortium RRID:SCR_003032 Drug Perturbation Enrichment algorithm (dpGSEA) Fang et al., 2021 RRID:SCR_025351 Limma package (Bioconducter) Ritchie et al., 2015 RRID:SCR_010943 Python v3.9.7 Python RRID:SCR_008394 (Continued on next page) e1 iScience 29, 115730, May 15, 2026 ..
Recombinant:Article Title: Single-cell Transcriptomics Reveal Altered B cell Responses and T cell Senescence in Geriatric Non-responders to COVID-19 mRNA Vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Human Phycoerythrin-conjugated Donkey F(ab)2 IgG, with Fcγ Jackson ImmunoResearch RRID: AB_2340519 Human monoclonal HLA-DR FITC Biolegend RRID: AB_314682 Human monoclonal CD19 APC eBioscience RRID: AB_10804519 Human monoclonal CD38 Alexa Fluor 700 Biolegend RRID: AB_2072781 Human monoclonal CD14 APC-Cy7 Biolegend RRID: AB_830693 Human monoclonal CD56 Pacific Blue Biolegend RRID: AB_10612566 Human monoclonal CD25 BV605 Biolegend RRID: AB_11218989 Human monoclonal CD8 BV786 BD RRID: AB_2687487 Human monoclonal PD-1 PE-Cy-7 Biolegend RRID: AB_2159324 Human monoclonal CD3 BUV395 BD RRID: AB_2744387 Human monoclonal CD45RA PE Texas Red Invitrogen RRID: AB_10372222 Human monoclonal CD74 BUV805 Biolegend RRID: AB_2075505 Human monoclonal CD4 BUV805 BD RRID: AB_2744423 Bacterial and virus strains Stabilized full-length S protein (aa 16-1230 with furin site mutated) Canaday et al., 2021 N/A SARS-CoV-2 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 D614G pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Phosphate-Buffered Saline (DPBS) Invitrogen Cat # 14190144 Bovine Serum Albumin (BSA) Invitrogen Cat # AM2616 RPMI (1640) Medium Corning Cat # 10-040-CV Fetal Bovine Serum Gibco Cat # 10438026 DMSO Sigma Cat # D2650-100ML Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3.1 10X Genomics Cat # 1000121 Chromium Next GEM Chip G Single Cell 10X Genomics Cat # 10001210 Single Index Kit N, Set A 10X Genomics Cat # 1000212 Live Dead Fixable Aqua Viability Kit Invitrogen Cat# NC0180395 Deposited data Processed single cell RNA-seq data Gene Expression Omnibus GSE300265 Software and algorithms Cellranger v4.0.0 10X Genomics RRID:SCR_0173 R (programming language) v4.1.1 R RRID:SCR_001905 Seurat R package v4.1.1 Hao et al. 2021 RRID:SCR_016341 Harmony R package v0.1.0 Broad Institute RRID:SCR_022206 ggplot2 R package R RRID:SCR_014601 BioRender BioRender RRID:SCR_018361 Gene Set Enrichment algorithm (GSEA) Broad Institute RRID:SCR_003199 Cytoscape v3.10.3 Cytoscape Consortium RRID:SCR_003032 Drug Perturbation Enrichment algorithm (dpGSEA) Fang et al., 2021 RRID:SCR_025351 Limma package (Bioconducter) Ritchie et al., 2015 RRID:SCR_010943 Python v3.9.7 Python RRID:SCR_008394 (Continued on next page) e1 iScience 29, 115730, May 15, 2026 ..
Article Title: Engineered intestinal crypt geometry uncovers YAP1-dependent fetal-to-adult transition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-E-Cadherin Clone 36/E-Cadherin (RUO) BD Bioscience 610181; RRID: AB_397580 CD44var (v6) Monoclonal Antibody (9A4) Invitrogen BMS145; RRID: AB_10597738 Lysozyme 1(EC.3.2.1.17) DAKO A0099; RRID: AB_2341231 EpCAM (Clone G8.8) ThermoFisher #17-5791-82; RRID: AB_2716944 BD PharmingenTM PE-CyTM7 Rat Anti-Mouse CD45 BD Bioscience 552848; RRID: AB_394489 CD31 (PECAM-1) Monoclonal Antibody (390), PE-Cyanine7 ThermoFisher 25-0311-82; RRID: AB_2869771 Keratin K20 Nordic Biosite/Progen 318-GP-K20; RRID: AB_1541036 YAP (D8H1X) Cell Signaling #14074; RRID: AB_2650491 Alexa Flour 488 Donkey anti Rabbit IgG (H+L) ThermoFisher A-21206 Alexa Fluor 488 Donkey anti Rat IgG (H+L) ThermoFisher A-21208 Alexa Fluor 555 Goat anti mouse IgG2a ThermoFisher A21137 Chemicals, peptides, and recombinant proteins 4-hydroxytamoxifen Sigma-Aldrich H6278 RapiClear 1.52 Sunjin Lab RC152002 Y-27632 dihydrochloride Sigma-Aldrich Y0503 N-Acetyl-L-cysteine Sigma-Aldrich A9165 Next-Generation Surrogate Wnt K. Christopher Garcia Miao et al. 55 Human EGF Peprotech AF-100-15 Murine Noggin Peprotech 250–38 R-spondin 1 conditioned medium in-house production N/A N2 Gibco 17502048 B27 Gibco 12587010 Diphtheria Toxin Merck D0564 Doxycycline hyclate Sigma-Aldrich D9891 Critical commercial assays TotalSeq hashtag antibodies Biolegend A0301, A0302, A0303, and A0304 Rneasy Micro Kit Qiagen 74004 Chromium Next GEM Single Cell 3 ′ Kit v3.1 10× Genomics PN-1000263 Library Construction Kit, 16 rxns 10× Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10× Genomics PN-1000287 Dual Index Kit TT Set A 10× Genomics PN-1000215 RNAscope Multiplex Fluorescent Reagent Kit v2 ACD Biotechne 323100 RNAscope probe mm-Atoh1 ACD Biotechne 408791-C3 RNAscope probe mm-Lyz1 ACD Biotechne 415131 Deposited data Single cell RNA-seq data This study GSE247255 scRNA-seq dataset from adult intestinal epithelium Haber et al. 29 GSE92332 scRNA-seq dataset from adult organoids Hansen et al. 32 GSE221278 scRNA-seq dataset from fetal progenitors Hansen et al. 32 GSE221278 Segmentation dataset and model This study https://zenodo.org/records/17565548 Experimental models: Organisms/strains C57BL/6J Taconic 17758-F Top.CFP Palle Serup Serup et al. 56 (Continued on next page) e1 Cell Stem Cell 33, 1–15.e1–e7, March 5, 2026 ..
Saline:Article Title: Single-cell Transcriptomics Reveal Altered B cell Responses and T cell Senescence in Geriatric Non-responders to COVID-19 mRNA Vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Human Phycoerythrin-conjugated Donkey F(ab)2 IgG, with Fcγ Jackson ImmunoResearch RRID: AB_2340519 Human monoclonal HLA-DR FITC Biolegend RRID: AB_314682 Human monoclonal CD19 APC eBioscience RRID: AB_10804519 Human monoclonal CD38 Alexa Fluor 700 Biolegend RRID: AB_2072781 Human monoclonal CD14 APC-Cy7 Biolegend RRID: AB_830693 Human monoclonal CD56 Pacific Blue Biolegend RRID: AB_10612566 Human monoclonal CD25 BV605 Biolegend RRID: AB_11218989 Human monoclonal CD8 BV786 BD RRID: AB_2687487 Human monoclonal PD-1 PE-Cy-7 Biolegend RRID: AB_2159324 Human monoclonal CD3 BUV395 BD RRID: AB_2744387 Human monoclonal CD45RA PE Texas Red Invitrogen RRID: AB_10372222 Human monoclonal CD74 BUV805 Biolegend RRID: AB_2075505 Human monoclonal CD4 BUV805 BD RRID: AB_2744423 Bacterial and virus strains Stabilized full-length S protein (aa 16-1230 with furin site mutated) Canaday et al., 2021 N/A SARS-CoV-2 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 D614G pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Phosphate-Buffered Saline (DPBS) Invitrogen Cat # 14190144 Bovine Serum Albumin (BSA) Invitrogen Cat # AM2616 RPMI (1640) Medium Corning Cat # 10-040-CV Fetal Bovine Serum Gibco Cat # 10438026 DMSO Sigma Cat # D2650-100ML Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3.1 10X Genomics Cat # 1000121 Chromium Next GEM Chip G Single Cell 10X Genomics Cat # 10001210 Single Index Kit N, Set A 10X Genomics Cat # 1000212 Live Dead Fixable Aqua Viability Kit Invitrogen Cat# NC0180395 Deposited data Processed single cell RNA-seq data Gene Expression Omnibus GSE300265 Software and algorithms Cellranger v4.0.0 10X Genomics RRID:SCR_0173 R (programming language) v4.1.1 R RRID:SCR_001905 Seurat R package v4.1.1 Hao et al. 2021 RRID:SCR_016341 Harmony R package v0.1.0 Broad Institute RRID:SCR_022206 ggplot2 R package R RRID:SCR_014601 BioRender BioRender RRID:SCR_018361 Gene Set Enrichment algorithm (GSEA) Broad Institute RRID:SCR_003199 Cytoscape v3.10.3 Cytoscape Consortium RRID:SCR_003032 Drug Perturbation Enrichment algorithm (dpGSEA) Fang et al., 2021 RRID:SCR_025351 Limma package (Bioconducter) Ritchie et al., 2015 RRID:SCR_010943 Python v3.9.7 Python RRID:SCR_008394 (Continued on next page) e1 iScience 29, 115730, May 15, 2026 ..
Single Cell RNA-Seq:Article Title: Single-cell Transcriptomics Reveal Altered B cell Responses and T cell Senescence in Geriatric Non-responders to COVID-19 mRNA Vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Human Phycoerythrin-conjugated Donkey F(ab)2 IgG, with Fcγ Jackson ImmunoResearch RRID: AB_2340519 Human monoclonal HLA-DR FITC Biolegend RRID: AB_314682 Human monoclonal CD19 APC eBioscience RRID: AB_10804519 Human monoclonal CD38 Alexa Fluor 700 Biolegend RRID: AB_2072781 Human monoclonal CD14 APC-Cy7 Biolegend RRID: AB_830693 Human monoclonal CD56 Pacific Blue Biolegend RRID: AB_10612566 Human monoclonal CD25 BV605 Biolegend RRID: AB_11218989 Human monoclonal CD8 BV786 BD RRID: AB_2687487 Human monoclonal PD-1 PE-Cy-7 Biolegend RRID: AB_2159324 Human monoclonal CD3 BUV395 BD RRID: AB_2744387 Human monoclonal CD45RA PE Texas Red Invitrogen RRID: AB_10372222 Human monoclonal CD74 BUV805 Biolegend RRID: AB_2075505 Human monoclonal CD4 BUV805 BD RRID: AB_2744423 Bacterial and virus strains Stabilized full-length S protein (aa 16-1230 with furin site mutated) Canaday et al., 2021 N/A SARS-CoV-2 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 D614G pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Phosphate-Buffered Saline (DPBS) Invitrogen Cat # 14190144 Bovine Serum Albumin (BSA) Invitrogen Cat # AM2616 RPMI (1640) Medium Corning Cat # 10-040-CV Fetal Bovine Serum Gibco Cat # 10438026 DMSO Sigma Cat # D2650-100ML Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3.1 10X Genomics Cat # 1000121 Chromium Next GEM Chip G Single Cell 10X Genomics Cat # 10001210 Single Index Kit N, Set A 10X Genomics Cat # 1000212 Live Dead Fixable Aqua Viability Kit Invitrogen Cat# NC0180395 Deposited data Processed single cell RNA-seq data Gene Expression Omnibus GSE300265 Software and algorithms Cellranger v4.0.0 10X Genomics RRID:SCR_0173 R (programming language) v4.1.1 R RRID:SCR_001905 Seurat R package v4.1.1 Hao et al. 2021 RRID:SCR_016341 Harmony R package v0.1.0 Broad Institute RRID:SCR_022206 ggplot2 R package R RRID:SCR_014601 BioRender BioRender RRID:SCR_018361 Gene Set Enrichment algorithm (GSEA) Broad Institute RRID:SCR_003199 Cytoscape v3.10.3 Cytoscape Consortium RRID:SCR_003032 Drug Perturbation Enrichment algorithm (dpGSEA) Fang et al., 2021 RRID:SCR_025351 Limma package (Bioconducter) Ritchie et al., 2015 RRID:SCR_010943 Python v3.9.7 Python RRID:SCR_008394 (Continued on next page) e1 iScience 29, 115730, May 15, 2026 ..
Article Title: In vivo evolution of antibody CR3022 expands cross-neutralization of SARS-CoV-2 variants and informs pan-sarbecovirus immunity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Sigma Adjuvant System (Ribi) Sigma Cat#S6322 LIVE/DEADTM Fixable Blue Dead Cell Stain Kit ThermoFisher Scientific Cat#L23105 7-AAD Biolegend Cat#420404 Buffer TCL 2X QIAGEN Cat#1070498 SuperScriptTM IV First-Strand Synthesis System ThermoFisher Scientific Cat#18091050 NextSeqTM1000/2000 P1/2 Reagents (300 cycles) Illumina Cat#20050264/20046812 SARS-CoV spike (6P) This manuscript N/A SARS-CoV-2 spike (6P) This manuscript N/A SARS-CoV RBD This manuscript N/A SARS-CoV-2 RBD This manuscript N/A Banal-52 RBD This manuscript N/A Alt-RTM S.p. .. Cas9 Nuclease V3 IDT Cat#1081058 EZ-Link sulfo-NHS-Biotin ThermoFisher Scientific Cat#A39256 Protein A resin GenScript Cat#L00210-50 Ni-NTA agarose beads Qiagen Cat#30230 Aquablue ELISA substrate ThermoFisher Scientific Cat#00-4203-58 Ophenylenediamine dihydrochloride (OPD) Sigma Cat#P9187-50SET Streptavidin-HRP Southern Biotech Cat#7105-05 Critical commercial assays Steady-Glo® Luciferase Assay System Promega Cat#E2550 Chromium Next GEM Single Cell 5′ Kit v2 10X Genomics Cat#1000263 Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat#1000286 Chromium Single Cell 5′ Feature Barcode Kit 10X Genomics Cat#1000256 Chromium Single Cell Mouse BCR Amplification Kit 10X Genomics Cat#1000255 Chromium Single cell Library Construction Kit 10X Genomics Cat#1000352 Deposited data Single cell RNA-seq datasets This manuscript GEO: GSE304367 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3 This manuscript PDB: 9PSN Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-622 and CC12.3 This manuscript PDB: 9PSO Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3 This manuscript PDB: 9PSP Experimental models: Cell lines Expi293F cells ThermoFisher Scientific Cat#14635 Vero E6 cells BEI Resources Cat#NR-54970 Sf9 cells ATCC Cat#CRL-1711; RRID: CVCL_0549 High Five cells Thermo Fisher Scientific Cat#B85502; RRID: CVCL_C190 Experimental models: Organisms/strains glCR3022H transgenic mouse This manuscript N/A C57BL/6 mouse Jackson lab Cat#000664 B6.SJL-Ptprca Pepcb/BoyJ Jackson lab Cat#002014 Oligonucleotides crRNA:tracrRNA IDT Cat#1072534 Mouse single-cell PCR primer sets von Boehmer et al.43 N/A (Continued on next page) 18 Cell Reports 45, 117137, April 28, 2026 .. Expi293F cells were maintained in Expi293 Expression Medium (Thermo Scientific) at 37◦C in a shaking incubator supplied with 8% CO2.
Article Title: Engineered intestinal crypt geometry uncovers YAP1-dependent fetal-to-adult transition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-E-Cadherin Clone 36/E-Cadherin (RUO) BD Bioscience 610181; RRID: AB_397580 CD44var (v6) Monoclonal Antibody (9A4) Invitrogen BMS145; RRID: AB_10597738 Lysozyme 1(EC.3.2.1.17) DAKO A0099; RRID: AB_2341231 EpCAM (Clone G8.8) ThermoFisher #17-5791-82; RRID: AB_2716944 BD PharmingenTM PE-CyTM7 Rat Anti-Mouse CD45 BD Bioscience 552848; RRID: AB_394489 CD31 (PECAM-1) Monoclonal Antibody (390), PE-Cyanine7 ThermoFisher 25-0311-82; RRID: AB_2869771 Keratin K20 Nordic Biosite/Progen 318-GP-K20; RRID: AB_1541036 YAP (D8H1X) Cell Signaling #14074; RRID: AB_2650491 Alexa Flour 488 Donkey anti Rabbit IgG (H+L) ThermoFisher A-21206 Alexa Fluor 488 Donkey anti Rat IgG (H+L) ThermoFisher A-21208 Alexa Fluor 555 Goat anti mouse IgG2a ThermoFisher A21137 Chemicals, peptides, and recombinant proteins 4-hydroxytamoxifen Sigma-Aldrich H6278 RapiClear 1.52 Sunjin Lab RC152002 Y-27632 dihydrochloride Sigma-Aldrich Y0503 N-Acetyl-L-cysteine Sigma-Aldrich A9165 Next-Generation Surrogate Wnt K. Christopher Garcia Miao et al. 55 Human EGF Peprotech AF-100-15 Murine Noggin Peprotech 250–38 R-spondin 1 conditioned medium in-house production N/A N2 Gibco 17502048 B27 Gibco 12587010 Diphtheria Toxin Merck D0564 Doxycycline hyclate Sigma-Aldrich D9891 Critical commercial assays TotalSeq hashtag antibodies Biolegend A0301, A0302, A0303, and A0304 Rneasy Micro Kit Qiagen 74004 Chromium Next GEM Single Cell 3 ′ Kit v3.1 10× Genomics PN-1000263 Library Construction Kit, 16 rxns 10× Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10× Genomics PN-1000287 Dual Index Kit TT Set A 10× Genomics PN-1000215 RNAscope Multiplex Fluorescent Reagent Kit v2 ACD Biotechne 323100 RNAscope probe mm-Atoh1 ACD Biotechne 408791-C3 RNAscope probe mm-Lyz1 ACD Biotechne 415131 Deposited data Single cell RNA-seq data This study GSE247255 scRNA-seq dataset from adult intestinal epithelium Haber et al. 29 GSE92332 scRNA-seq dataset from adult organoids Hansen et al. 32 GSE221278 scRNA-seq dataset from fetal progenitors Hansen et al. 32 GSE221278 Segmentation dataset and model This study https://zenodo.org/records/17565548 Experimental models: Organisms/strains C57BL/6J Taconic 17758-F Top.CFP Palle Serup Serup et al. 56 (Continued on next page) e1 Cell Stem Cell 33, 1–15.e1–e7, March 5, 2026 ..
Gene Expression:Article Title: Single-cell Transcriptomics Reveal Altered B cell Responses and T cell Senescence in Geriatric Non-responders to COVID-19 mRNA Vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Human Phycoerythrin-conjugated Donkey F(ab)2 IgG, with Fcγ Jackson ImmunoResearch RRID: AB_2340519 Human monoclonal HLA-DR FITC Biolegend RRID: AB_314682 Human monoclonal CD19 APC eBioscience RRID: AB_10804519 Human monoclonal CD38 Alexa Fluor 700 Biolegend RRID: AB_2072781 Human monoclonal CD14 APC-Cy7 Biolegend RRID: AB_830693 Human monoclonal CD56 Pacific Blue Biolegend RRID: AB_10612566 Human monoclonal CD25 BV605 Biolegend RRID: AB_11218989 Human monoclonal CD8 BV786 BD RRID: AB_2687487 Human monoclonal PD-1 PE-Cy-7 Biolegend RRID: AB_2159324 Human monoclonal CD3 BUV395 BD RRID: AB_2744387 Human monoclonal CD45RA PE Texas Red Invitrogen RRID: AB_10372222 Human monoclonal CD74 BUV805 Biolegend RRID: AB_2075505 Human monoclonal CD4 BUV805 BD RRID: AB_2744423 Bacterial and virus strains Stabilized full-length S protein (aa 16-1230 with furin site mutated) Canaday et al., 2021 N/A SARS-CoV-2 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 D614G pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Phosphate-Buffered Saline (DPBS) Invitrogen Cat # 14190144 Bovine Serum Albumin (BSA) Invitrogen Cat # AM2616 RPMI (1640) Medium Corning Cat # 10-040-CV Fetal Bovine Serum Gibco Cat # 10438026 DMSO Sigma Cat # D2650-100ML Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3.1 10X Genomics Cat # 1000121 Chromium Next GEM Chip G Single Cell 10X Genomics Cat # 10001210 Single Index Kit N, Set A 10X Genomics Cat # 1000212 Live Dead Fixable Aqua Viability Kit Invitrogen Cat# NC0180395 Deposited data Processed single cell RNA-seq data Gene Expression Omnibus GSE300265 Software and algorithms Cellranger v4.0.0 10X Genomics RRID:SCR_0173 R (programming language) v4.1.1 R RRID:SCR_001905 Seurat R package v4.1.1 Hao et al. 2021 RRID:SCR_016341 Harmony R package v0.1.0 Broad Institute RRID:SCR_022206 ggplot2 R package R RRID:SCR_014601 BioRender BioRender RRID:SCR_018361 Gene Set Enrichment algorithm (GSEA) Broad Institute RRID:SCR_003199 Cytoscape v3.10.3 Cytoscape Consortium RRID:SCR_003032 Drug Perturbation Enrichment algorithm (dpGSEA) Fang et al., 2021 RRID:SCR_025351 Limma package (Bioconducter) Ritchie et al., 2015 RRID:SCR_010943 Python v3.9.7 Python RRID:SCR_008394 (Continued on next page) e1 iScience 29, 115730, May 15, 2026 ..
Software:Article Title: Single-cell Transcriptomics Reveal Altered B cell Responses and T cell Senescence in Geriatric Non-responders to COVID-19 mRNA Vaccination
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Human Phycoerythrin-conjugated Donkey F(ab)2 IgG, with Fcγ Jackson ImmunoResearch RRID: AB_2340519 Human monoclonal HLA-DR FITC Biolegend RRID: AB_314682 Human monoclonal CD19 APC eBioscience RRID: AB_10804519 Human monoclonal CD38 Alexa Fluor 700 Biolegend RRID: AB_2072781 Human monoclonal CD14 APC-Cy7 Biolegend RRID: AB_830693 Human monoclonal CD56 Pacific Blue Biolegend RRID: AB_10612566 Human monoclonal CD25 BV605 Biolegend RRID: AB_11218989 Human monoclonal CD8 BV786 BD RRID: AB_2687487 Human monoclonal PD-1 PE-Cy-7 Biolegend RRID: AB_2159324 Human monoclonal CD3 BUV395 BD RRID: AB_2744387 Human monoclonal CD45RA PE Texas Red Invitrogen RRID: AB_10372222 Human monoclonal CD74 BUV805 Biolegend RRID: AB_2075505 Human monoclonal CD4 BUV805 BD RRID: AB_2744423 Bacterial and virus strains Stabilized full-length S protein (aa 16-1230 with furin site mutated) Canaday et al., 2021 N/A SARS-CoV-2 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A SARS-CoV-2 ΔC18 D614G pseudotyped pHAGE-CMV-Luc2-IRES-ZsGreen-W lentivirus Wilfredo et al., 2021 N/A Chemicals, peptides, and recombinant proteins Dulbecco’s Phosphate-Buffered Saline (DPBS) Invitrogen Cat # 14190144 Bovine Serum Albumin (BSA) Invitrogen Cat # AM2616 RPMI (1640) Medium Corning Cat # 10-040-CV Fetal Bovine Serum Gibco Cat # 10438026 DMSO Sigma Cat # D2650-100ML Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3.1 10X Genomics Cat # 1000121 Chromium Next GEM Chip G Single Cell 10X Genomics Cat # 10001210 Single Index Kit N, Set A 10X Genomics Cat # 1000212 Live Dead Fixable Aqua Viability Kit Invitrogen Cat# NC0180395 Deposited data Processed single cell RNA-seq data Gene Expression Omnibus GSE300265 Software and algorithms Cellranger v4.0.0 10X Genomics RRID:SCR_0173 R (programming language) v4.1.1 R RRID:SCR_001905 Seurat R package v4.1.1 Hao et al. 2021 RRID:SCR_016341 Harmony R package v0.1.0 Broad Institute RRID:SCR_022206 ggplot2 R package R RRID:SCR_014601 BioRender BioRender RRID:SCR_018361 Gene Set Enrichment algorithm (GSEA) Broad Institute RRID:SCR_003199 Cytoscape v3.10.3 Cytoscape Consortium RRID:SCR_003032 Drug Perturbation Enrichment algorithm (dpGSEA) Fang et al., 2021 RRID:SCR_025351 Limma package (Bioconducter) Ritchie et al., 2015 RRID:SCR_010943 Python v3.9.7 Python RRID:SCR_008394 (Continued on next page) e1 iScience 29, 115730, May 15, 2026 ..
Enzyme-linked Immunosorbent Assay:Article Title: In vivo evolution of antibody CR3022 expands cross-neutralization of SARS-CoV-2 variants and informs pan-sarbecovirus immunity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Sigma Adjuvant System (Ribi) Sigma Cat#S6322 LIVE/DEADTM Fixable Blue Dead Cell Stain Kit ThermoFisher Scientific Cat#L23105 7-AAD Biolegend Cat#420404 Buffer TCL 2X QIAGEN Cat#1070498 SuperScriptTM IV First-Strand Synthesis System ThermoFisher Scientific Cat#18091050 NextSeqTM1000/2000 P1/2 Reagents (300 cycles) Illumina Cat#20050264/20046812 SARS-CoV spike (6P) This manuscript N/A SARS-CoV-2 spike (6P) This manuscript N/A SARS-CoV RBD This manuscript N/A SARS-CoV-2 RBD This manuscript N/A Banal-52 RBD This manuscript N/A Alt-RTM S.p. .. Cas9 Nuclease V3 IDT Cat#1081058 EZ-Link sulfo-NHS-Biotin ThermoFisher Scientific Cat#A39256 Protein A resin GenScript Cat#L00210-50 Ni-NTA agarose beads Qiagen Cat#30230 Aquablue ELISA substrate ThermoFisher Scientific Cat#00-4203-58 Ophenylenediamine dihydrochloride (OPD) Sigma Cat#P9187-50SET Streptavidin-HRP Southern Biotech Cat#7105-05 Critical commercial assays Steady-Glo® Luciferase Assay System Promega Cat#E2550 Chromium Next GEM Single Cell 5′ Kit v2 10X Genomics Cat#1000263 Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat#1000286 Chromium Single Cell 5′ Feature Barcode Kit 10X Genomics Cat#1000256 Chromium Single Cell Mouse BCR Amplification Kit 10X Genomics Cat#1000255 Chromium Single cell Library Construction Kit 10X Genomics Cat#1000352 Deposited data Single cell RNA-seq datasets This manuscript GEO: GSE304367 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3 This manuscript PDB: 9PSN Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-622 and CC12.3 This manuscript PDB: 9PSO Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3 This manuscript PDB: 9PSP Experimental models: Cell lines Expi293F cells ThermoFisher Scientific Cat#14635 Vero E6 cells BEI Resources Cat#NR-54970 Sf9 cells ATCC Cat#CRL-1711; RRID: CVCL_0549 High Five cells Thermo Fisher Scientific Cat#B85502; RRID: CVCL_C190 Experimental models: Organisms/strains glCR3022H transgenic mouse This manuscript N/A C57BL/6 mouse Jackson lab Cat#000664 B6.SJL-Ptprca Pepcb/BoyJ Jackson lab Cat#002014 Oligonucleotides crRNA:tracrRNA IDT Cat#1072534 Mouse single-cell PCR primer sets von Boehmer et al.43 N/A (Continued on next page) 18 Cell Reports 45, 117137, April 28, 2026 .. Expi293F cells were maintained in Expi293 Expression Medium (Thermo Scientific) at 37◦C in a shaking incubator supplied with 8% CO2.
Luciferase:Article Title: In vivo evolution of antibody CR3022 expands cross-neutralization of SARS-CoV-2 variants and informs pan-sarbecovirus immunity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Sigma Adjuvant System (Ribi) Sigma Cat#S6322 LIVE/DEADTM Fixable Blue Dead Cell Stain Kit ThermoFisher Scientific Cat#L23105 7-AAD Biolegend Cat#420404 Buffer TCL 2X QIAGEN Cat#1070498 SuperScriptTM IV First-Strand Synthesis System ThermoFisher Scientific Cat#18091050 NextSeqTM1000/2000 P1/2 Reagents (300 cycles) Illumina Cat#20050264/20046812 SARS-CoV spike (6P) This manuscript N/A SARS-CoV-2 spike (6P) This manuscript N/A SARS-CoV RBD This manuscript N/A SARS-CoV-2 RBD This manuscript N/A Banal-52 RBD This manuscript N/A Alt-RTM S.p. .. Cas9 Nuclease V3 IDT Cat#1081058 EZ-Link sulfo-NHS-Biotin ThermoFisher Scientific Cat#A39256 Protein A resin GenScript Cat#L00210-50 Ni-NTA agarose beads Qiagen Cat#30230 Aquablue ELISA substrate ThermoFisher Scientific Cat#00-4203-58 Ophenylenediamine dihydrochloride (OPD) Sigma Cat#P9187-50SET Streptavidin-HRP Southern Biotech Cat#7105-05 Critical commercial assays Steady-Glo® Luciferase Assay System Promega Cat#E2550 Chromium Next GEM Single Cell 5′ Kit v2 10X Genomics Cat#1000263 Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat#1000286 Chromium Single Cell 5′ Feature Barcode Kit 10X Genomics Cat#1000256 Chromium Single Cell Mouse BCR Amplification Kit 10X Genomics Cat#1000255 Chromium Single cell Library Construction Kit 10X Genomics Cat#1000352 Deposited data Single cell RNA-seq datasets This manuscript GEO: GSE304367 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3 This manuscript PDB: 9PSN Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-622 and CC12.3 This manuscript PDB: 9PSO Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3 This manuscript PDB: 9PSP Experimental models: Cell lines Expi293F cells ThermoFisher Scientific Cat#14635 Vero E6 cells BEI Resources Cat#NR-54970 Sf9 cells ATCC Cat#CRL-1711; RRID: CVCL_0549 High Five cells Thermo Fisher Scientific Cat#B85502; RRID: CVCL_C190 Experimental models: Organisms/strains glCR3022H transgenic mouse This manuscript N/A C57BL/6 mouse Jackson lab Cat#000664 B6.SJL-Ptprca Pepcb/BoyJ Jackson lab Cat#002014 Oligonucleotides crRNA:tracrRNA IDT Cat#1072534 Mouse single-cell PCR primer sets von Boehmer et al.43 N/A (Continued on next page) 18 Cell Reports 45, 117137, April 28, 2026 .. Expi293F cells were maintained in Expi293 Expression Medium (Thermo Scientific) at 37◦C in a shaking incubator supplied with 8% CO2.
Amplification:Article Title: In vivo evolution of antibody CR3022 expands cross-neutralization of SARS-CoV-2 variants and informs pan-sarbecovirus immunity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Sigma Adjuvant System (Ribi) Sigma Cat#S6322 LIVE/DEADTM Fixable Blue Dead Cell Stain Kit ThermoFisher Scientific Cat#L23105 7-AAD Biolegend Cat#420404 Buffer TCL 2X QIAGEN Cat#1070498 SuperScriptTM IV First-Strand Synthesis System ThermoFisher Scientific Cat#18091050 NextSeqTM1000/2000 P1/2 Reagents (300 cycles) Illumina Cat#20050264/20046812 SARS-CoV spike (6P) This manuscript N/A SARS-CoV-2 spike (6P) This manuscript N/A SARS-CoV RBD This manuscript N/A SARS-CoV-2 RBD This manuscript N/A Banal-52 RBD This manuscript N/A Alt-RTM S.p. .. Cas9 Nuclease V3 IDT Cat#1081058 EZ-Link sulfo-NHS-Biotin ThermoFisher Scientific Cat#A39256 Protein A resin GenScript Cat#L00210-50 Ni-NTA agarose beads Qiagen Cat#30230 Aquablue ELISA substrate ThermoFisher Scientific Cat#00-4203-58 Ophenylenediamine dihydrochloride (OPD) Sigma Cat#P9187-50SET Streptavidin-HRP Southern Biotech Cat#7105-05 Critical commercial assays Steady-Glo® Luciferase Assay System Promega Cat#E2550 Chromium Next GEM Single Cell 5′ Kit v2 10X Genomics Cat#1000263 Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat#1000286 Chromium Single Cell 5′ Feature Barcode Kit 10X Genomics Cat#1000256 Chromium Single Cell Mouse BCR Amplification Kit 10X Genomics Cat#1000255 Chromium Single cell Library Construction Kit 10X Genomics Cat#1000352 Deposited data Single cell RNA-seq datasets This manuscript GEO: GSE304367 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3 This manuscript PDB: 9PSN Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-622 and CC12.3 This manuscript PDB: 9PSO Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3 This manuscript PDB: 9PSP Experimental models: Cell lines Expi293F cells ThermoFisher Scientific Cat#14635 Vero E6 cells BEI Resources Cat#NR-54970 Sf9 cells ATCC Cat#CRL-1711; RRID: CVCL_0549 High Five cells Thermo Fisher Scientific Cat#B85502; RRID: CVCL_C190 Experimental models: Organisms/strains glCR3022H transgenic mouse This manuscript N/A C57BL/6 mouse Jackson lab Cat#000664 B6.SJL-Ptprca Pepcb/BoyJ Jackson lab Cat#002014 Oligonucleotides crRNA:tracrRNA IDT Cat#1072534 Mouse single-cell PCR primer sets von Boehmer et al.43 N/A (Continued on next page) 18 Cell Reports 45, 117137, April 28, 2026 .. Expi293F cells were maintained in Expi293 Expression Medium (Thermo Scientific) at 37◦C in a shaking incubator supplied with 8% CO2.
Binding Assay:Article Title: In vivo evolution of antibody CR3022 expands cross-neutralization of SARS-CoV-2 variants and informs pan-sarbecovirus immunity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Sigma Adjuvant System (Ribi) Sigma Cat#S6322 LIVE/DEADTM Fixable Blue Dead Cell Stain Kit ThermoFisher Scientific Cat#L23105 7-AAD Biolegend Cat#420404 Buffer TCL 2X QIAGEN Cat#1070498 SuperScriptTM IV First-Strand Synthesis System ThermoFisher Scientific Cat#18091050 NextSeqTM1000/2000 P1/2 Reagents (300 cycles) Illumina Cat#20050264/20046812 SARS-CoV spike (6P) This manuscript N/A SARS-CoV-2 spike (6P) This manuscript N/A SARS-CoV RBD This manuscript N/A SARS-CoV-2 RBD This manuscript N/A Banal-52 RBD This manuscript N/A Alt-RTM S.p. .. Cas9 Nuclease V3 IDT Cat#1081058 EZ-Link sulfo-NHS-Biotin ThermoFisher Scientific Cat#A39256 Protein A resin GenScript Cat#L00210-50 Ni-NTA agarose beads Qiagen Cat#30230 Aquablue ELISA substrate ThermoFisher Scientific Cat#00-4203-58 Ophenylenediamine dihydrochloride (OPD) Sigma Cat#P9187-50SET Streptavidin-HRP Southern Biotech Cat#7105-05 Critical commercial assays Steady-Glo® Luciferase Assay System Promega Cat#E2550 Chromium Next GEM Single Cell 5′ Kit v2 10X Genomics Cat#1000263 Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat#1000286 Chromium Single Cell 5′ Feature Barcode Kit 10X Genomics Cat#1000256 Chromium Single Cell Mouse BCR Amplification Kit 10X Genomics Cat#1000255 Chromium Single cell Library Construction Kit 10X Genomics Cat#1000352 Deposited data Single cell RNA-seq datasets This manuscript GEO: GSE304367 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3 This manuscript PDB: 9PSN Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-622 and CC12.3 This manuscript PDB: 9PSO Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3 This manuscript PDB: 9PSP Experimental models: Cell lines Expi293F cells ThermoFisher Scientific Cat#14635 Vero E6 cells BEI Resources Cat#NR-54970 Sf9 cells ATCC Cat#CRL-1711; RRID: CVCL_0549 High Five cells Thermo Fisher Scientific Cat#B85502; RRID: CVCL_C190 Experimental models: Organisms/strains glCR3022H transgenic mouse This manuscript N/A C57BL/6 mouse Jackson lab Cat#000664 B6.SJL-Ptprca Pepcb/BoyJ Jackson lab Cat#002014 Oligonucleotides crRNA:tracrRNA IDT Cat#1072534 Mouse single-cell PCR primer sets von Boehmer et al.43 N/A (Continued on next page) 18 Cell Reports 45, 117137, April 28, 2026 .. Expi293F cells were maintained in Expi293 Expression Medium (Thermo Scientific) at 37◦C in a shaking incubator supplied with 8% CO2.
Transgenic Assay:Article Title: In vivo evolution of antibody CR3022 expands cross-neutralization of SARS-CoV-2 variants and informs pan-sarbecovirus immunity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Sigma Adjuvant System (Ribi) Sigma Cat#S6322 LIVE/DEADTM Fixable Blue Dead Cell Stain Kit ThermoFisher Scientific Cat#L23105 7-AAD Biolegend Cat#420404 Buffer TCL 2X QIAGEN Cat#1070498 SuperScriptTM IV First-Strand Synthesis System ThermoFisher Scientific Cat#18091050 NextSeqTM1000/2000 P1/2 Reagents (300 cycles) Illumina Cat#20050264/20046812 SARS-CoV spike (6P) This manuscript N/A SARS-CoV-2 spike (6P) This manuscript N/A SARS-CoV RBD This manuscript N/A SARS-CoV-2 RBD This manuscript N/A Banal-52 RBD This manuscript N/A Alt-RTM S.p. .. Cas9 Nuclease V3 IDT Cat#1081058 EZ-Link sulfo-NHS-Biotin ThermoFisher Scientific Cat#A39256 Protein A resin GenScript Cat#L00210-50 Ni-NTA agarose beads Qiagen Cat#30230 Aquablue ELISA substrate ThermoFisher Scientific Cat#00-4203-58 Ophenylenediamine dihydrochloride (OPD) Sigma Cat#P9187-50SET Streptavidin-HRP Southern Biotech Cat#7105-05 Critical commercial assays Steady-Glo® Luciferase Assay System Promega Cat#E2550 Chromium Next GEM Single Cell 5′ Kit v2 10X Genomics Cat#1000263 Chromium Next GEM Chip K Single Cell Kit 10X Genomics Cat#1000286 Chromium Single Cell 5′ Feature Barcode Kit 10X Genomics Cat#1000256 Chromium Single Cell Mouse BCR Amplification Kit 10X Genomics Cat#1000255 Chromium Single cell Library Construction Kit 10X Genomics Cat#1000352 Deposited data Single cell RNA-seq datasets This manuscript GEO: GSE304367 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3 This manuscript PDB: 9PSN Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-622 and CC12.3 This manuscript PDB: 9PSO Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3 This manuscript PDB: 9PSP Experimental models: Cell lines Expi293F cells ThermoFisher Scientific Cat#14635 Vero E6 cells BEI Resources Cat#NR-54970 Sf9 cells ATCC Cat#CRL-1711; RRID: CVCL_0549 High Five cells Thermo Fisher Scientific Cat#B85502; RRID: CVCL_C190 Experimental models: Organisms/strains glCR3022H transgenic mouse This manuscript N/A C57BL/6 mouse Jackson lab Cat#000664 B6.SJL-Ptprca Pepcb/BoyJ Jackson lab Cat#002014 Oligonucleotides crRNA:tracrRNA IDT Cat#1072534 Mouse single-cell PCR primer sets von Boehmer et al.43 N/A (Continued on next page) 18 Cell Reports 45, 117137, April 28, 2026 .. Expi293F cells were maintained in Expi293 Expression Medium (Thermo Scientific) at 37◦C in a shaking incubator supplied with 8% CO2.
RNAscope:Article Title: Engineered intestinal crypt geometry uncovers YAP1-dependent fetal-to-adult transition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-E-Cadherin Clone 36/E-Cadherin (RUO) BD Bioscience 610181; RRID: AB_397580 CD44var (v6) Monoclonal Antibody (9A4) Invitrogen BMS145; RRID: AB_10597738 Lysozyme 1(EC.3.2.1.17) DAKO A0099; RRID: AB_2341231 EpCAM (Clone G8.8) ThermoFisher #17-5791-82; RRID: AB_2716944 BD PharmingenTM PE-CyTM7 Rat Anti-Mouse CD45 BD Bioscience 552848; RRID: AB_394489 CD31 (PECAM-1) Monoclonal Antibody (390), PE-Cyanine7 ThermoFisher 25-0311-82; RRID: AB_2869771 Keratin K20 Nordic Biosite/Progen 318-GP-K20; RRID: AB_1541036 YAP (D8H1X) Cell Signaling #14074; RRID: AB_2650491 Alexa Flour 488 Donkey anti Rabbit IgG (H+L) ThermoFisher A-21206 Alexa Fluor 488 Donkey anti Rat IgG (H+L) ThermoFisher A-21208 Alexa Fluor 555 Goat anti mouse IgG2a ThermoFisher A21137 Chemicals, peptides, and recombinant proteins 4-hydroxytamoxifen Sigma-Aldrich H6278 RapiClear 1.52 Sunjin Lab RC152002 Y-27632 dihydrochloride Sigma-Aldrich Y0503 N-Acetyl-L-cysteine Sigma-Aldrich A9165 Next-Generation Surrogate Wnt K. Christopher Garcia Miao et al. 55 Human EGF Peprotech AF-100-15 Murine Noggin Peprotech 250–38 R-spondin 1 conditioned medium in-house production N/A N2 Gibco 17502048 B27 Gibco 12587010 Diphtheria Toxin Merck D0564 Doxycycline hyclate Sigma-Aldrich D9891 Critical commercial assays TotalSeq hashtag antibodies Biolegend A0301, A0302, A0303, and A0304 Rneasy Micro Kit Qiagen 74004 Chromium Next GEM Single Cell 3 ′ Kit v3.1 10× Genomics PN-1000263 Library Construction Kit, 16 rxns 10× Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10× Genomics PN-1000287 Dual Index Kit TT Set A 10× Genomics PN-1000215 RNAscope Multiplex Fluorescent Reagent Kit v2 ACD Biotechne 323100 RNAscope probe mm-Atoh1 ACD Biotechne 408791-C3 RNAscope probe mm-Lyz1 ACD Biotechne 415131 Deposited data Single cell RNA-seq data This study GSE247255 scRNA-seq dataset from adult intestinal epithelium Haber et al. 29 GSE92332 scRNA-seq dataset from adult organoids Hansen et al. 32 GSE221278 scRNA-seq dataset from fetal progenitors Hansen et al. 32 GSE221278 Segmentation dataset and model This study https://zenodo.org/records/17565548 Experimental models: Organisms/strains C57BL/6J Taconic 17758-F Top.CFP Palle Serup Serup et al. 56 (Continued on next page) e1 Cell Stem Cell 33, 1–15.e1–e7, March 5, 2026 ..
Multiplex Assay:Article Title: Engineered intestinal crypt geometry uncovers YAP1-dependent fetal-to-adult transition.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-E-Cadherin Clone 36/E-Cadherin (RUO) BD Bioscience 610181; RRID: AB_397580 CD44var (v6) Monoclonal Antibody (9A4) Invitrogen BMS145; RRID: AB_10597738 Lysozyme 1(EC.3.2.1.17) DAKO A0099; RRID: AB_2341231 EpCAM (Clone G8.8) ThermoFisher #17-5791-82; RRID: AB_2716944 BD PharmingenTM PE-CyTM7 Rat Anti-Mouse CD45 BD Bioscience 552848; RRID: AB_394489 CD31 (PECAM-1) Monoclonal Antibody (390), PE-Cyanine7 ThermoFisher 25-0311-82; RRID: AB_2869771 Keratin K20 Nordic Biosite/Progen 318-GP-K20; RRID: AB_1541036 YAP (D8H1X) Cell Signaling #14074; RRID: AB_2650491 Alexa Flour 488 Donkey anti Rabbit IgG (H+L) ThermoFisher A-21206 Alexa Fluor 488 Donkey anti Rat IgG (H+L) ThermoFisher A-21208 Alexa Fluor 555 Goat anti mouse IgG2a ThermoFisher A21137 Chemicals, peptides, and recombinant proteins 4-hydroxytamoxifen Sigma-Aldrich H6278 RapiClear 1.52 Sunjin Lab RC152002 Y-27632 dihydrochloride Sigma-Aldrich Y0503 N-Acetyl-L-cysteine Sigma-Aldrich A9165 Next-Generation Surrogate Wnt K. Christopher Garcia Miao et al. 55 Human EGF Peprotech AF-100-15 Murine Noggin Peprotech 250–38 R-spondin 1 conditioned medium in-house production N/A N2 Gibco 17502048 B27 Gibco 12587010 Diphtheria Toxin Merck D0564 Doxycycline hyclate Sigma-Aldrich D9891 Critical commercial assays TotalSeq hashtag antibodies Biolegend A0301, A0302, A0303, and A0304 Rneasy Micro Kit Qiagen 74004 Chromium Next GEM Single Cell 3 ′ Kit v3.1 10× Genomics PN-1000263 Library Construction Kit, 16 rxns 10× Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10× Genomics PN-1000287 Dual Index Kit TT Set A 10× Genomics PN-1000215 RNAscope Multiplex Fluorescent Reagent Kit v2 ACD Biotechne 323100 RNAscope probe mm-Atoh1 ACD Biotechne 408791-C3 RNAscope probe mm-Lyz1 ACD Biotechne 415131 Deposited data Single cell RNA-seq data This study GSE247255 scRNA-seq dataset from adult intestinal epithelium Haber et al. 29 GSE92332 scRNA-seq dataset from adult organoids Hansen et al. 32 GSE221278 scRNA-seq dataset from fetal progenitors Hansen et al. 32 GSE221278 Segmentation dataset and model This study https://zenodo.org/records/17565548 Experimental models: Organisms/strains C57BL/6J Taconic 17758-F Top.CFP Palle Serup Serup et al. 56 (Continued on next page) e1 Cell Stem Cell 33, 1–15.e1–e7, March 5, 2026 ..
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