Virus:Article Title: Cadherins modulate the self-organizing potential of pseudo-embryos.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat Monoclonal Ab anti E-Cadherin Abcam (Abcam Cat# ab11512, RRID:AB_298118) Rabbit Monoclonal Ab anti N-Cadherin Cell Signaling Technology (Cell Signaling Technology Cat# 13116, RRID:AB_2687616) Goat Polyclonal Ab anti TBX6 R&D system (R and D Systems Cat# AF4744, RRID:AB_2200834) Goat Polyclonal Ab anti SOX2 R&D system (R and D Systems Cat# AF2018, RRID:AB_355110) Rabbit Monoclonal Ab anti SOX2 Cell Signaling Technology (Cell Signaling Technology Cat# 23064, RRID:AB_2714146) Rabbit Polyclonal Ab anti FOXC1 Abcam (Abcam Cat# ab223850, RRID:AB_2848202) Rabbit Polyclonal Ab anti T/BRACHYURY Abcam (Abcam Cat# ab209665, RRID:AB_2750925) Rabbit Monoclonal Ab anti SNAI1 Cell Signaling Technology (Cell Signaling Technology Cat# 3879, RRID:AB_2255011) Phalloidin-iFluor 488nm Abcam ab176753 Donkey anti-Goat IgG Alexa 568nm Thermo-Fisher (Thermo Fisher Scientific Cat# A-11057, RRID:AB_2534104) Donkey anti-Rat IgG Alexa 488nm Thermo-Fisher (Thermo Fisher Scientific Cat# A-21208, RRID:AB_2535794) Donkey anti-Rabbit IgG Alexa 647nm Thermo-Fisher (Thermo Fisher Scientific Cat# A-31573, RRID:AB_2536183) Bacterial and virus strains DH5α Competent E. coli New England Biolab C2987H Chemicals, peptides, and recombinant proteins DMEM + Glutamax Gibco Cat# 16141-079 Sodium pyruvate Gibco Cat# 1360-039 B- mercaptoethanol Gibco Cat# 31350-010 penicillin/streptomycin Gibco Cat# 15140-122 LIF EPFL PTPSP Core Facility N/A GSK3 inhibitor (CHIR99021) Biozol Cat# FBM-10-1279-5MG MEK1/2 inhibitor (PD0325901) Selleckchem Cat# S1036 PBS Gibco Cat# 10010023 ES certified FBS Gibco Cat# 16141079 Accutase StemPro Cat# A11105-01 Glutamax Gibco Cat# 35050061 DMEM/F12 medium Gibco Cat# 11320033 Neurobasal medium Gibco Cat# 21103049 N2 supplement Gibco Cat# 17502048 B27 supplement Gibco Cat# 17504044 Matrigel Corning Cat# 356230 RAPIClear 1.52 SUNJin Lan Cat# RC152001 Proteinase K Eurobio Cat# GEXPRK00-6R alkaline phosphatase Roche Cat# 3359123001 BM-Purple Roche Cat# 11442074001 (Continued on next page) 16 Cell Reports 44, 116567, November 25, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays RNeasy mini kit Qiagen Cat# 74104 Qiaquick PCR purification kit Qiagen Cat# 28106 Deposited data ATAC-seq This study GSE247507 RNA-seq This study GSE247508 scRNA-seq This study GSE247509 Re-analysis of GSE106227 Beccari et al. 201811 GSE247510 SuperSeries This study GSE247511 Experimental models: Cell lines 129/svev Embryomax CMTI-1 (RRID:CVCL_GS41) 129/svev Mesp2:mCherry reporter line This study N/A 129/svev Snai1− /− This study N/A 129/svev Cdh2− /+ This study N/A 129/svev Cdh2− /− This study N/A Oligonucleotides See Tables S2, S3, and S4 This study N/A Recombinant DNA eSpCas9(1.1)-T2A-Puro Addgene Addgene: #101039 Mesp-del5′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A Mesp-del3′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A Mesp2-sgRNA eSpCas9(1.1)-T2A-Puro This study N/A Snai1-del5′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A Snai1-del3′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A Cdh2-del5′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A Cdh2-del3′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A pUC57-Mesp2HA-p2a-mCherry-NLS This study N/A Software and algorithms Code and Analysis pipeline This study N/A ImageJ v1.54f Schindelin et al., 201260 https://doi.org/10.1038/nmeth.2019 iLastik v1.4.0rc5 Berg et al., 201961 https://doi.org/10.1038/s41592-019- 0582-9 JACOP v1.2.0 Bolte and Cordelières, 200662 https://doi.org/10.1111/j.1365-2818.2006.
Recombinant:Article Title: Cadherins modulate the self-organizing potential of pseudo-embryos.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat Monoclonal Ab anti E-Cadherin Abcam (Abcam Cat# ab11512, RRID:AB_298118) Rabbit Monoclonal Ab anti N-Cadherin Cell Signaling Technology (Cell Signaling Technology Cat# 13116, RRID:AB_2687616) Goat Polyclonal Ab anti TBX6 R&D system (R and D Systems Cat# AF4744, RRID:AB_2200834) Goat Polyclonal Ab anti SOX2 R&D system (R and D Systems Cat# AF2018, RRID:AB_355110) Rabbit Monoclonal Ab anti SOX2 Cell Signaling Technology (Cell Signaling Technology Cat# 23064, RRID:AB_2714146) Rabbit Polyclonal Ab anti FOXC1 Abcam (Abcam Cat# ab223850, RRID:AB_2848202) Rabbit Polyclonal Ab anti T/BRACHYURY Abcam (Abcam Cat# ab209665, RRID:AB_2750925) Rabbit Monoclonal Ab anti SNAI1 Cell Signaling Technology (Cell Signaling Technology Cat# 3879, RRID:AB_2255011) Phalloidin-iFluor 488nm Abcam ab176753 Donkey anti-Goat IgG Alexa 568nm Thermo-Fisher (Thermo Fisher Scientific Cat# A-11057, RRID:AB_2534104) Donkey anti-Rat IgG Alexa 488nm Thermo-Fisher (Thermo Fisher Scientific Cat# A-21208, RRID:AB_2535794) Donkey anti-Rabbit IgG Alexa 647nm Thermo-Fisher (Thermo Fisher Scientific Cat# A-31573, RRID:AB_2536183) Bacterial and virus strains DH5α Competent E. coli New England Biolab C2987H Chemicals, peptides, and recombinant proteins DMEM + Glutamax Gibco Cat# 16141-079 Sodium pyruvate Gibco Cat# 1360-039 B- mercaptoethanol Gibco Cat# 31350-010 penicillin/streptomycin Gibco Cat# 15140-122 LIF EPFL PTPSP Core Facility N/A GSK3 inhibitor (CHIR99021) Biozol Cat# FBM-10-1279-5MG MEK1/2 inhibitor (PD0325901) Selleckchem Cat# S1036 PBS Gibco Cat# 10010023 ES certified FBS Gibco Cat# 16141079 Accutase StemPro Cat# A11105-01 Glutamax Gibco Cat# 35050061 DMEM/F12 medium Gibco Cat# 11320033 Neurobasal medium Gibco Cat# 21103049 N2 supplement Gibco Cat# 17502048 B27 supplement Gibco Cat# 17504044 Matrigel Corning Cat# 356230 RAPIClear 1.52 SUNJin Lan Cat# RC152001 Proteinase K Eurobio Cat# GEXPRK00-6R alkaline phosphatase Roche Cat# 3359123001 BM-Purple Roche Cat# 11442074001 (Continued on next page) 16 Cell Reports 44, 116567, November 25, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER Critical commercial assays RNeasy mini kit Qiagen Cat# 74104 Qiaquick PCR purification kit Qiagen Cat# 28106 Deposited data ATAC-seq This study GSE247507 RNA-seq This study GSE247508 scRNA-seq This study GSE247509 Re-analysis of GSE106227 Beccari et al. 201811 GSE247510 SuperSeries This study GSE247511 Experimental models: Cell lines 129/svev Embryomax CMTI-1 (RRID:CVCL_GS41) 129/svev Mesp2:mCherry reporter line This study N/A 129/svev Snai1− /− This study N/A 129/svev Cdh2− /+ This study N/A 129/svev Cdh2− /− This study N/A Oligonucleotides See Tables S2, S3, and S4 This study N/A Recombinant DNA eSpCas9(1.1)-T2A-Puro Addgene Addgene: #101039 Mesp-del5′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A Mesp-del3′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A Mesp2-sgRNA eSpCas9(1.1)-T2A-Puro This study N/A Snai1-del5′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A Snai1-del3′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A Cdh2-del5′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A Cdh2-del3′-sgRNA eSpCas9(1.1)T2A-Puro This study N/A pUC57-Mesp2HA-p2a-mCherry-NLS This study N/A Software and algorithms Code and Analysis pipeline This study N/A ImageJ v1.54f Schindelin et al., 201260 https://doi.org/10.1038/nmeth.2019 iLastik v1.4.0rc5 Berg et al., 201961 https://doi.org/10.1038/s41592-019- 0582-9 JACOP v1.2.0 Bolte and Cordelières, 200662 https://doi.org/10.1111/j.1365-2818.2006.
Article Title: Generation of dorsoventral human spinal cord organoids via functionalizing composite scaffold for drug testing.
Article Snippet: .. Antibodies PAX6 Biolegend Cat# 901301 NKX6.1 Developmental Studies Hybridoma Bank Cat# F55A12 MAP2 Cell Signaling Technology Cat# 4542S Olig2 Millipore Cat# AB9610 ChAT Millipore Cat# AB144P HB9 Developmental Studies Hybridoma Bank Cat# 81.5C10-S Lhx1 Developmental Studies Hybridoma Bank Cat# 4F2-S Lhx3 Developmental Studies Hybridoma Bank Cat# 67.4E12 Olig3 Sigma-Aldrich Cat# HPA018303 Tuj-1 Biolegend Cat# 801201 GAD67 Millipore Cat# MAB5406 VGlut1 UC Davids/NIH NeuroMab Cat# 75-066 Hoxc9 Abcam Cat# ab50839 Hox10 Santa Cruz Biotechnology Cat# SC-365519 Caspase3 Cell Signaling Technology Cat# 9661S NeuN Abcam Cat# ab104224 GFAP Abcam Cat# ab7260 MBP Biolegend Cat# 808401 OCT4 BD Biosciences Cat# 561555 SOX2 Cell Signaling Technology Cat# 4900S SSEA4 Millipore Cat# MAB4304 TRA-1-60 Millipore Cat# MAB4306 Chemicals, peptides, and recombinant proteins Chitosan Macklin Cat# C850348 Glacial acetic acid Macklin Cat# A801295 S80 Macklin Cat# S817933 Tween-60 Macklin Cat# T819614 Dimethyl sulfoxide Sigma-Aldrich Cat# D8418 SAG MedChemExpress Cat# HY-12848 Matrigel Corning Cat# 356230 FGF PeproTech Cat# AF-100-18B TGF-b Cell Signaling Technology Cat# 8915LF b-mercaptoethanol Sigma-Aldrich Cat# M3148 .. CHIR99021 Tocris Cat# 4423
Western Blot:Article Title: Betaine inhibits the stem cell-like properties of hepatocellular carcinoma by activating autophagy via SAM/m 6 A/YTHDF1-mediated enhancement on ATG3 stability
Article Snippet: .. E-cadherin ABclonal A20798 1:1000 N-cadherin ABclonal A19083 1:2000 Vimentin ABclonal A19607 1:10000 MMP2 ABclonal A6247 1:500 CD133 Cell Signaling technology 64326 1:1000 for WB, 1:500 for IF CD44 ABclonal A19020 1:1000 EpCAM ABclonal A19301 1:10000 SOX2 Cell Signaling technology 23064 1:1000 Nanog Cell Signaling technology 4903 1:1000 for WB, 1:200 for IF Ki-67 ABclonal A26200 1:500 PCNA ABclonal A12427 1:1000 LC3B Cell Signaling technology 2775 1:1000 LC3B Cell Signaling technology 83506 1:400 for IF ATG3 Cell Signaling technology 3415 1:1000 ATG5 ABclonal A19677 1:1000 BHMT ABclonal A5134 1:1000 YTHDF1 Cell Signaling technology 57530 1:1000 m6A ABclonal A19841 1:1000 ACTB ABclonal AC038 1:10000 .. IgG (H+L) Jackson ImmunoResearch 115-025-062 1:100
other:Article Title: Impaired KDM2B-mediated PRC1 recruitment to chromatin causes defective neural stem cell self-renewal and ASD/ID-like behaviors.
Article Snippet: Antibodies Rabbit monoclonal anti Sox2 Cell signaling technology Cat#:3728, lot 4; RRID: AB_2194037 Rabbit monoclonal anti-GFAP Cell signaling technology Cat#: 12389, lot 5; RRID: AB_2631098 Rat monoclonal anti-BrdU Bio-rad MCA2060; RRID: AB_323427 Rabbit polyclonal anti-KDM2B Dr. Robert Klose (Oxford University) N/A Rabbit monoclonal anti-RING1B Cell signaling technology Cat#: 5694, lot 1; RRID: AB_10705604 Rabbit polyclonal anti-TUBULIN alpha Proteintech Cat#: 11224-1-AP; RRID: AB_2210206
Article Title: SNRPB-mediated RNA splicing drives tumor cell proliferation and stemness in hepatocellular carcinoma.
Article Snippet: ID Antibodies Corporations Catalog Dilutions 1 SNRPB Santa Cruz Biotechnology #sc-271094 1:1,000 2 CD133 Cell Signaling Technology #64326 1:1,000 3 AFP Cell Signaling Technology #4448 1:1,000 4 CK19 Cell Signaling Technology #4558 1:1,000 5 Nanog Cell Signaling Technology #4903 1:2,000 6 Sox2 Cell Signaling Technology #3579 1:1,000 7 Phospho-Akt (Ser473) Cell Signaling Technology #4060 1:1,000 8 Akt (pan) Cell Signaling Technology #4685 1:1,000 9 Akt3 Cell Signaling Technology #3788 1:1,000 10 β-Actin Cell Signaling Technology #3700 1:2,000
Concentration Assay:Article Title: MSCs act as biopatches for blood-retinal barrier preservation to enhance functional recovery after retinal I/R
Article Snippet: .. Antibody Source Concentration CCL5 Invitrogen 710001 1:200 Nanog Cell Signaling Technology 4903 1:200 Sox2 Cell Signaling Technology 3579 1:400 Oct4 Cell Signaling Technology 2750 1:200 Claudin5 Invitrogen 35-2500 1:200 Fibrinogen Abcam ab34269 1:200 NG2 Sigma-Aldrich AB5320 1:200 Ter119 Invitrogen 14-5921-82 1:200 ZO-1 Invitrogen 33-9100 1:100 F4/80 Abcam ab6640 1:200 TUNEL kit Thermo Fisher Scientific C10617 1 test Isolectin GS-IB4 conjugated to Alexa Fluor 488 Invitrogen I21411 1:100 Isolectin GS-IB4 conjugated to Alexa Fluor 594 Invitrogen I21413 1:100 Alexa Fluor® 555 conjugated goat anti-mouse IgG Invitrogen A-21422 1:500 Alexa Fluor® 555 conjugated goat anti-rabbit IgG Invitrogen A-21428 1:500 Alexa Fluor® 555 conjugated goat anti-rat IgG Invitrogen A-21434 1:500 Alexa Fluor® 647 conjugated goat anti-mouse IgG Invitrogen A-21240 1:500 12 Table. .. S2 Antibodies used for Flow cytometry analysis Antibody Source Concentration CD29 Biolegend 303001 1:100 CD44 Biolegend 397502 1:100 CD73 Biolegend 344002 1:100 CD90 Biolegend 328101 1:100 CD34 Biolegend 343501 1:100 CD45 Biolegend 304001 1:100 CCL5 Biolegend 149103 1:100 CCR5 Invitrogen 14-1957-82 1:100 13 Table.
Article Title: MSCs act as biopatches for blood-retinal barrier preservation to enhance functional recovery after retinal I/R
Article Snippet: .. Antibody Source Concentration CCL5 Invitrogen 710001 1:200 Nanog Cell Signaling Technology 4903 1:200 Sox2 Cell Signaling Technology 3579 1:400 Oct4 Cell Signaling Technology 2750 1:200 Claudin5 Invitrogen 35-2500 1:200 Fibrinogen Abcam ab34269 1:200 NG2 Sigma-Aldrich AB5320 1:200 Ter119 Invitrogen 14-5921-82 1:200 ZO-1 Invitrogen 33-9100 1:100 F4/80 Abcam ab6640 1:200 TUNEL kit Thermo Fisher Scientific C10617 1 test Isolectin GS-IB4 conjugated to Alexa Fluor 488 Invitrogen I21411 1:100 Isolectin GS-IB4 conjugated to Alexa Fluor 594 Invitrogen I21413 1:100 Alexa Fluor® 555 conjugated goat anti-mouse IgG Invitrogen A-21422 1:500 Alexa Fluor® 555 conjugated goat anti-rabbit IgG Invitrogen A-21428 1:500 Alexa Fluor® 555 conjugated goat anti-rat IgG Invitrogen A-21434 1:500 Alexa Fluor® 647 conjugated goat anti-mouse IgG Invitrogen A-21240 1:500 12 Table. .. S2 Antibodies used for Flow cytometry analysis Antibody Source Concentration CD29 Biolegend 303001 1:100 CD44 Biolegend 397502 1:100 CD73 Biolegend 344002 1:100 CD90 Biolegend 328101 1:100 CD34 Biolegend 343501 1:100 CD45 Biolegend 304001 1:100 CCL5 Biolegend 149103 1:100 CCR5 Invitrogen 14-1957-82 1:100 13 Table.
TUNEL Assay:Article Title: MSCs act as biopatches for blood-retinal barrier preservation to enhance functional recovery after retinal I/R
Article Snippet: .. Antibody Source Concentration CCL5 Invitrogen 710001 1:200 Nanog Cell Signaling Technology 4903 1:200 Sox2 Cell Signaling Technology 3579 1:400 Oct4 Cell Signaling Technology 2750 1:200 Claudin5 Invitrogen 35-2500 1:200 Fibrinogen Abcam ab34269 1:200 NG2 Sigma-Aldrich AB5320 1:200 Ter119 Invitrogen 14-5921-82 1:200 ZO-1 Invitrogen 33-9100 1:100 F4/80 Abcam ab6640 1:200 TUNEL kit Thermo Fisher Scientific C10617 1 test Isolectin GS-IB4 conjugated to Alexa Fluor 488 Invitrogen I21411 1:100 Isolectin GS-IB4 conjugated to Alexa Fluor 594 Invitrogen I21413 1:100 Alexa Fluor® 555 conjugated goat anti-mouse IgG Invitrogen A-21422 1:500 Alexa Fluor® 555 conjugated goat anti-rabbit IgG Invitrogen A-21428 1:500 Alexa Fluor® 555 conjugated goat anti-rat IgG Invitrogen A-21434 1:500 Alexa Fluor® 647 conjugated goat anti-mouse IgG Invitrogen A-21240 1:500 12 Table. .. S2 Antibodies used for Flow cytometry analysis Antibody Source Concentration CD29 Biolegend 303001 1:100 CD44 Biolegend 397502 1:100 CD73 Biolegend 344002 1:100 CD90 Biolegend 328101 1:100 CD34 Biolegend 343501 1:100 CD45 Biolegend 304001 1:100 CCL5 Biolegend 149103 1:100 CCR5 Invitrogen 14-1957-82 1:100 13 Table.
Article Title: MSCs act as biopatches for blood-retinal barrier preservation to enhance functional recovery after retinal I/R
Article Snippet: .. Antibody Source Concentration CCL5 Invitrogen 710001 1:200 Nanog Cell Signaling Technology 4903 1:200 Sox2 Cell Signaling Technology 3579 1:400 Oct4 Cell Signaling Technology 2750 1:200 Claudin5 Invitrogen 35-2500 1:200 Fibrinogen Abcam ab34269 1:200 NG2 Sigma-Aldrich AB5320 1:200 Ter119 Invitrogen 14-5921-82 1:200 ZO-1 Invitrogen 33-9100 1:100 F4/80 Abcam ab6640 1:200 TUNEL kit Thermo Fisher Scientific C10617 1 test Isolectin GS-IB4 conjugated to Alexa Fluor 488 Invitrogen I21411 1:100 Isolectin GS-IB4 conjugated to Alexa Fluor 594 Invitrogen I21413 1:100 Alexa Fluor® 555 conjugated goat anti-mouse IgG Invitrogen A-21422 1:500 Alexa Fluor® 555 conjugated goat anti-rabbit IgG Invitrogen A-21428 1:500 Alexa Fluor® 555 conjugated goat anti-rat IgG Invitrogen A-21434 1:500 Alexa Fluor® 647 conjugated goat anti-mouse IgG Invitrogen A-21240 1:500 12 Table. .. S2 Antibodies used for Flow cytometry analysis Antibody Source Concentration CD29 Biolegend 303001 1:100 CD44 Biolegend 397502 1:100 CD73 Biolegend 344002 1:100 CD90 Biolegend 328101 1:100 CD34 Biolegend 343501 1:100 CD45 Biolegend 304001 1:100 CCL5 Biolegend 149103 1:100 CCR5 Invitrogen 14-1957-82 1:100 13 Table.
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