Reagents and tools table
| Reagent and resource | Source | Identifier | |
|---|---|---|---|
| Antibodies | |||
| Globo-H (VK9) | Thermo Fisher Scientific (mouse, monoclonal) (FACS, IHC-Fr, IF) | 14-9700-82 | |
| NANOG | Abcam (rabbit, monoclonal) (FACS) | Ab214549 | |
| SSEA3 | Santa Cruz Biotechnology (rat, monoclonal) (FACS) | sc-21703 | |
| SSEA4 | Santa Cruz Biotechnology (rat, monoclonal) (FACS, IF) | sc-21704 | |
| SSEA5 APC | Biolegend (mouse, monoclonal) (FACS) | 355209 | |
| OCT3/4 | Santa Cruz Biotechnology (mouse, monoclonal) (FACS) | sc-5279 | |
| TRA-1-60 | R&D Systems (mouse, monoclonal) (IF) | MAB4770 | |
| SOX2 | GeneTex (mouse, monoclonal) (FACS) | GTX627404 | |
| Brachyury | Santa Cruz Biotechnology (goat, polyclonal) (IHC-Fr) | sc-17743 | |
| FT1 (human) | Thermo Fisher Scientific (rabbit, polyclonal) (FACS) | PA5-13515 | |
| FT1 (mouse) | LifeSpan BioSciences (rabbit polyclonal) (IHC-Fr) | LS-C407806 | |
| MIXL1 | Mercury (rabbit, polyclonal) (IHC-Fr) | ABS232 | |
| CDX2 AF 488 | Abcam (rabbit, polyclonal) (IHC-Fr) | ab195007 | |
| HAND1 | R&D Systems (goat, polyclonal) (FACS) | AF3168 | |
| HOPX | Abcam (rabbit, monoclonal) (FACS) | Ab106251 | |
| NKX2.5 | Santa Cruz Biotechnology (mouse, monoclonal) (FACS) | sc-376565 | |
| PAX6 | Thermo Fisher Scientific (rabbit, polyclonal) (FACS, IF) | 42-6600 | |
| OTX2 AF488 | R&D Systems (mouse, monoclonal) (IHC-Fr) | IC979G | |
| SOX17 | Abcam (mouse, monoclonal) (FACS) | Ab84990 | |
| SIRPA APC | Biolegend (mouse, monoclonal) (FACS, IF) | 323810 | |
| cTnT | Abcam (rabbit, monoclonal) (FACS, IF) | Ab8295 | |
| Cardiac myosin | GeneTex (mouse, monoclonal) (FACS, IF) | GTX20015 | |
| Sarcomeric-α actinin | Sigma-Aldrich-Merck (mouse, monoclonal) (IF) | A7811 | |
| Phospho-SMAD1/5/9 | Cell Signaling Technology (rabbit, monoclonal) (FACS, Western blotting) | 13820 | |
| α-Fetoprotein (αFP) | R&D Systems (mouse, monoclonal) (FACS) | MAB1368 | |
| HRP-β-Actin | Santa Cruz Biotechnology (mouse, nonoclonal) (Western blotting) | SC-47778 | |
| Chemicals, Proteins, and Factors | |||
| FGF-basic | PeproTech (Recombinant human protein) | 100-18B | |
| BMP4 | PeproTech (Recombinant human protein) | 120-05 | |
| LDN193189 | BioGems | 1062443 | |
| CHIR 99021 | Tocris | 4423 | |
| Wnt-3a | PeproTech (Recombinant murine protein) | 315-20 | |
| Activin-A | PeproTech (Recombinant human/murine/rat protein) | 120-14 | |
| IWP-2 | Tocris (WNT inhibitor) | 3533 | |
| Dorsomorphin | Tocris (BMP type I receptor inhibitor) | 3093 | |
| A-83-01 | BioGems (TGF-β type I receptor inhibitor) | 9094360 | |
| Retinoic acid | Sigma-Aldrich-Merck | R2625 | |
| ROCK inhibitor Y-27632 | Cayman Chemical | 10005583 | |
| Phalloidin AF488 | Thermo Fisher Scientific (IF for F-actin staining) | A12379 | |
| UEA-I biotinylated | Vector Laboratories | B-1065-2 | |
| siRNA sequences | |||
| Target gene | Duplex sequence | IDT duplex name | |
| HPRT |
5′-GCCAGACUUUGUUGGAUUGGAAA-3′ 5′-AAUUUCAAAUCCAACAAAGUCUGGCUU-3′ |
HPRT-S1 DS | |
| NC-1 |
5′-CGUUAAUCGCGUAUAAUACGUGUA-3′ 5′-AUACGCGUAUUAUACGCGAUUAACGAC-3′ |
NC1 control duplex | |
| NC-2 |
5′-CUUCCUCUCUUUCUCUCCCUUGUGA-3′ 5′-UCACAAGGGAGAGAAAGAGAGGAAGGA-3′ |
NC2 | |
| FUT1 |
5′-GGGAGUUACAGUUACAAUUGUUACA-3′ 5′-UGUAACAAUUGUAACUGUAACUCCCUG-3′ |
NM_000148 duplex1 | |
| FUT1 |
5′-GGAAGACAGGUUGGCUAAUUUCCTG-3′ 5′-CAGGAAAUUAGCCAACCUGUCUUCCCU-3′ |
NM_000148 duplex2 | |
| FUT1 |
5′-UCCAGAUAACUAAGGUGAAGAAUCT-3′ 5′-AGAUUCUUCACCUUAGUUAUCUGGAUU-3′ |
NM_000148 duplex3 | |
| FUT1 |
5′-CCACUCUGGACAUUGGCUAAGCCTT-3′ 5′-AAGGCUUAGCCAAUGUCCAGAGUGGAG-3′ |
NM_000148 13.2 | |
| FUT1 |
5′-UUGAGAGAUCCUUUCCUGAAGCUCT-3′ 5′-AGAGCUUCAGGAAAGGAUCUCUCAAGU-3′ |
NM_000148 13.3 | |
| Recombinant DNA (Plasmids) | |||
| pHAGE2-FullEF1A-DsRedExpress-IRES-ZsGreen | This paper | ||
| pHAGE2-FullEF1A-FUT1Express-IRES-ZsGreen | This paper | ||
| Critical Commercial Assays | |||
| Lipofectamine RNAiMAX transfection reagent | Thermo Fisher Scientific | 13778075 | |
| Deposited Data | |||
| RNA-Seq |
Li et al (2014) |
GEO: GDS5003 | |
| Sc-RNA-Seq |
Peng et al (2019) https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120963 |
GEO: GSE120963 | |
| RNA-Seq |
Gu et al (2014) |
GEO: GSE48257 | |
| RNA-Seq |
Loh et al (2016) |
GEO: GSE85066 | |
| RNA-Seq |
Loh et al (2014) |
GEO: GSE52657 | |
| RNA-Seq |
This paper |
PRJNA1112109 | |
| Raw data |
This paper https://www.ebi.ac.uk/biostudies/studies/S-BSST1426?key=22235c8f-e525-455c-8b88-053d58da8348 |
Biostudies, accession number S-BSST1426 | |
| Cell lines | |||
| WA09 hESC | WiCell | RRID:CVCL_9773 | |
| WA09.1 hESC | WiCell | RRID:CVCL_C811 | |
| WIBR1 hESC | Whitehead Institute | RRID:CVCL_9765 | |
| WIBR2 hESC | Whitehead Institute | RRID:CVCL_9766 | |
| BJ hiPSC | BGU | RRID:CVCL_A4YN | |
| EMF hiPSC | BGU | RRID:CVCL_A4ZP | |
| OME hiPSC | BGU | RRID:CVCL_A4YM | |
| WA09 hESC FUT1 | This paper | Overexpression of FUT1 | |
| WA09 hESC Control | This paper | Mock-transfected hESCs | |
| Software and Algorithms | |||
| 2D, 3D plots | Peng G, Suo S, Cui G, Yu F, Wang R, Chen J, Chen S, Liu Z, Chen G, Qian Y, et al (2019) | http://egastrulation.sibcb.ac.cn | |
| FUT1 sequences (primers) | |||
| Sequences | |||
| Forward | 5′-GCAGCGGCCGCCTAGCCTGCCCTGGGTGAA-3′ | ||
| Reverse | 5′-TTAGGATCCTTCTAGAACTGCCTGCCAGC-3′ | ||
| TaqMan assay data for qPCR | |||
| Standard gene name | Full gene name | Gene product | TaqMan gene expression assay ID |
| GAPDH | Glyceraldehyde-3-phosphate dehydrogenase | GAPDH | Hs99999905_m1 |
| ACTB | Actin beta | Actin beta | Hs99999903_m1 |
| HPRT | hypoxanthine phosphoribosyltransferase 1 | HPRT | Hs99999909_m1 |
| POU5F1 | POU class 5 homeobox 1 | OCT4 | Hs04260367_gH |
| NANOG | Nanog homeobox | NANOG | Hs04399610_g1 |
| SOX2 | SRY-box Transcription Factor 2 | SOX2 | Hs01053049_s1 |
| SOX1 | SRY-Box Transcription Factor 1 | SOX1 | Hs01057642_s1 |
| GATA4 | GATA binding protein 4 | GATA4 | Hs00171403_m1 |
| NKX2.5 | NK2 homeobox 5 | NKX2.5 | Hs00231763_m1 |
| ISL1 | ISL LIM homeobox 1 | ISL1 | Hs00158126_m1 |
| TNNT2 | Troponin T cardiac type 2 | Troponin T | Hs00943911_m1 |
| ACTC1 | Actin Alpha Cardiac Muscle 1 | Alpha-Cardiac Actin | Hs01109515_m1 |
| FUT1 | fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase) | FUT1 | Hs01379722_m1 |
| FUT1 | Fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase) | FUT1 plasmid | Hs00355741_m1 |
| FUT2 | Fucosyltransferase 2 (galactoside 2-alpha-L-fucosyltransferase 2) | FUT2 | Hs00704693_s1 |
| FUT3 | Blood group Lewis alpha-4-fucosyltransferase | FUT3 | Hs00356857_m1 |
| B3GALT2 | UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase; polypeptide 2 | B3GALT2 | Hs00705203_s1 |
| B3GALNT1 | Beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group) | B3GALNT1 | Hs00364202_s1 |
| B3GNT5 | UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5 | B3GNT5 | Hs00908059_m1 |
| UGCG | UDP-glucose ceramide glucosyltransferase | Glucosylceramide synthase | Hs00234293_m1 |
| ST3GAL1 | ST3 beta-galactoside alpha-2,3-sialyltransferase 1 | ST3GAL1 | Hs00161688_m1 |
| HOPX | HOP homeobox | HOPX | Hs04188695_m1 |
| FOXF1 | Forkhead box F1 | FOXF1 | Hs00230962_m1 |
| IRX3 | Iroquois homeobox 3 | IRX3 | Hs01124217_g1 |
| SMAD4 | SMAD family member 4 | SMAD4 | Hs00929647_m1 |
| PAX6 | Paired box 6 | PAX6 | Hs00240871_m1 |
| FOXA2 | Forkhead box A2 | FOXA2 | Hs00232764_m1 |
| SOX17 | SRY-box transcription factor 17 | SOX17 | Hs00751752_s1 |
| AXIN1 | Axin 1 | AXIN1 | Hs00959582_m1 |
| MSGN1 | Mesogenin 1 | MSGN1 | Hs03405514_s1 |
| HHEX | Hematopoietically-expressed homeobox | HHEX | Hs01074519_m1 |
| T | T Brachyury transcription factor | BRY | Hs00610080_m1 |
| MESP1 | Mesoderm posterior protein 1 | MESP1 | Hs00251489_m1 |
| OTX2 | Orthodenticle homeobox 2 | OTX2 | Hs00222238_m1 |
| VIM | Vimentin | Vimentin | Hs00185584_m1 |
| KI67 | Marker of proliferation Ki67 | MKI76 | Hs01032443_m1 |
| Cyclin D1 | B-cell lymphoma 1 protein | CCND1 | Hs00277039_m1 |