| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-CD31 | Novus Biologicals | Cat# NB100-2284; RRID:AB_10002513 |
| Armenian Hamster monoclonal anti-CD31 | DSHB | Cat# 2H8; RRID:AB_21610393 |
| Mouse monoclonal anti-CD31 | Cell Signaling | Cat# 3528S; RRID:AB_2160882 |
| Goat polyclonal anti-Choline Acetyltransferase | Millipore | Cat# AB144P; RRID:AB_2079751 |
| Mouse monoclonal anti-Collagen 1 | Abcam | Cat# ab6308; RRID:AB_305411 |
| Rabbit monoclonal anti-Collagen 1 | Abcam | Cat# ab138492; RRID:AB_2861258 |
| Mouse monoclonal anti-Collagen 2 | Abcam | Cat# ab185430; RRID:AB_1603612 |
| Goat polyclonal anti-Lyve1 | R&D systems | Cat# AF2089; RRID:AB_355144 |
| Mouse monoclonal anti-Myosin Heavy Chain | Millipore | Cat# 05-716; RRID:AB_309930 |
| MHC coupled Vio-667 | Miltenyi | N/A (not yet commercialised) |
| Rabbit polyclonal anti-MyH3 | Invitrogen | Cat# PA5-72848; RRID:AB_2718702 |
| Rabbit monoclonal anti-MyoD1 | Abcam | Cat# ab133627; RRID:AB_2890928 |
| Mouse monoclonal anti-Myogenin | Abcam | Cat# ab1835; RRID:AB_302633 |
| Mouse monoclonal anti-Neurofilament-H conjugated to Alexa 488 | Biolegend | Cat# 801612 RRID:AB_2750330 |
| Rabbit monoclonal anti-Osterix | Abcam | Cat# ab209484; RRID:AB_2892207 |
| Rabbit polyclonal anti-Pax7 | Invitrogen | Cat# PA1-117; RRID:AB_2539886 |
| Mouse monoclonal anti-Pax7 | Abcam | Cat# ab218472; RRID:N/A |
| Mouse monoclonal anti-Peripherin | Millipore | Cat# MAB1527; RRID:AB_2284441 |
| Mouse monoclonal anti-PLVAP | Abcam | Cat# ab81719; RRID:AB_1658370 |
| Rabbit monoclonal anti-Prox1 | Abcam | Cat# ab199359; RRID:AB_2868427 |
| Rabbit polyclonal anti-SMA | Abcam | Cat# ab5694; RRID:AB_2223021 |
| Rabbit monoclonal anti-SMA | Abcam | Cat# ab32575; RRID:AB_722538 |
| Rabbit monoclonal anti-SMA conjugated to Alexa488 | Abcam | Cat# ab202295; RRID:AB_2890884 |
| Rabbit monoclonal anti-SMA conjugated to Alexa 555 | Abcam | Cat# ab202509; RRID:AB_2868435 |
| Rabbit monoclonal anti-SMA conjugated to Alexa 594 | Abcam | Cat# ab202510; RRID:N/A |
| Rabbit monoclonal anti-SMA conjugated to Alexa 647 | Abcam | Cat# ab202296; RRID:N/A |
| Goat polyclonal anti-Sox9 | R&D systems | Cat# AF3075; RRID:AB_2194160 |
| Rabbit monoclonal anti-Sox9 conjugated to Alexa647 | Abcam | Cat# ab207677; RRID:N/A |
| Rabbit monoclonal anti-Synaptophysin | Abcam | Cat# ab32127; RRID:AB_2286949 |
| Rabbit monoclonal anti-Synaptophysin conjugated to Alexa 647 | Abcam | Cat# ab196166; RRID:N/A |
| Goat polyclonal anti-Tag1/Contactin2 | R&D Systems | Cat# AF4439; RRID:AB_2044647 |
| Rabbit polyclonal anti-Tenomodulin | Abcam | Cat# ab203676; RRID:AB_2722782 |
| Sheep polyclonal anti-Tyrosine Hydroxylase | Invitrogen | Cat# PA1-4679; RRID:AB_561880 |
| Mouse monoclonal anti-Tubulin beta III | Abcam | Cat# ab78078; RRID:AB_2256751 |
| Rabbit polyclonal anti-Tubulin beta III | Sigma-Aldrich | Cat# T2200; RRID:AB_262133 |
| Donkey Anti-Rabbit IgG H&L (Alexa Fluor 488) | Abcam | Cat# ab150073; RRID:AB_2636877 |
| Donkey Anti-Rabbit IgG H&L (Alexa Fluor 555) | Abcam | Cat# ab150062; RRID:AB_2801638 |
| Donkey Anti-Rabbit IgG H&L (Alexa Fluor 647) | Abcam | Cat# ab150063; RRID:AB_2687541 |
| Donkey Anti-Rabbit IgG H&L (Alexa Fluor 790) | Abcam | Cat# ab186693; RRID:N/A |
| Donkey Anti-Goat IgG H&L (Alexa Fluor 488) | Abcam | Cat# ab150129; RRID:AB_2687506 |
| Donkey Anti-Goat IgG H&L (Cy3) | Abcam | Cat# ab6949; RRID:AB_955018 |
| Donkey Anti-Goat IgG H&L (Alexa Fluor 647) | Abcam | Cat# ab150135; RRID:AB_2687955 |
| Donkey Anti-Goat IgG H&L (Alexa Fluor 750) | Abcam | Cat# ab175745; RRID:AB_2924800 |
| Donkey Anti-Mouse IgG H&L (Alexa Fluor 488) | Abcam | Cat# ab150105; RRID:AB_2732856 |
| Donkey Anti-MouseIgG H&L (Alexa Fluor 555) | Abcam | Cat# ab150110; RRID:AB_2783637 |
| Donkey Anti-Mouse IgG H&L (Alexa Fluor 647) | Abcam | Cat# ab150111; RRID:AB_2890625 |
| Donkey Anti-Mouse IgG H&L (Alexa Fluor 790) | Abcam | Cat# ab186699; RRID:N/A |
| Donkey Anti-Sheep IgG H&L (Alexa Fluor 790) | Jackson ImmunoResearch Labs | Cat# 137327; RRID:N/A |
| Goat Anti-Armenian Hamster IgG H&L (Alexa Fluor 488) | Abcam | Cat# ab173003; RRID:AB_2936402 |
| Biological samples | ||
| Human tissues | INSERM-Hudeca Biobank | this paper |
| Chemicals, peptides, and recombinant proteins | ||
| Phosphate-Buffered Saline | Sigma-Aldrich | Cat# D1408-500ml |
| Helix NP Green | Biolegend | Cat# 425303;RRID:N/A |
| bisBenzimide H (DAPI) | Sigma-Aldrich | Cat# 33258 |
| Agarose | Carl ROTH | Cat# 2267.4 |
| Azide | Sigma-Aldrich | Cat# S2002 |
| Dibenzyl ether (DBE) | Sigma-Aldrich | Cat# 108014 |
| Dichloromethane (DCM) | Sigma-Aldrich | Cat# 270997 |
| Ethylenediaminetetraacetic acid (EDTA) | Sigma-Aldrich | Cat# E7889 |
| Formalin | Sigma-Aldrich | Cat# HT501128 |
| Gelatin | VWR Chemicals | Cat# 24350.262 |
| Hydrogen peroxide solution (H2O2) | Sigma-Aldrich | Cat# 216763 |
| Isopentane | VWR Chemicals | Cat# 24872.298 |
| Methanol (MeOH) | VWR Chemicals | Cat# 20847.360 |
| Mowiol | Sigma-Aldrich | Cat# 81381 |
| Paraformaldehyde | VWR Chemicals | Cat# 28794.295 |
| Polystyrene Weighing dishes | Sigma-Aldrich | Cat# Z154873; Z15488; Z154903 |
| Single Edge Razor Blade | Electron Microscopy Sciences | Cat# 71972 |
| Slides BOND Plus | Leica Biosystems | Cat# S21.2113.A |
| Sucrose | VWR Chemicals | Cat# 27478.296 |
| Syringe filters ROTILABO® MCE, 0,22 μm | Carl ROTH | Cat# KH54.1 |
| TAE Buffer 10X | Invitrogen | Cat# 15558-026 |
| Thimerosal | Sigma-Aldrich | Cat# T8784-5g |
| Thimerosal | Sigma-Aldrich | Cat# T5125 |
| Triton X100 | Sigma-Aldrich | Cat# X100-500ml |
| Tube TPP 15 & 50 mL | Dutscher | Cat# 191115; 191050 |
| Vannas Spring Scissors | Fine Science Tool | Cat# 15000-03 |
| Oligonucleotides | ||
| SRY sense 5′-AGCGATGATTACAGTCCAGC-3′ | Belle et al.19 | N/A |
| SRY antisense 5′-CCTACAGCTTTGTCCAGTGG-3′ | Belle et al.19 | N/A |
| FGF16 sense 5′- CGGGAGGGATACAGGACTAAAC-3′ | Belle et al.19 | N/A |
| FGF16 antisense 5′- CTGTAGGTAGCATCTGTGGC-3′ | Belle et al.19 | N/A |
| Deposited Data | ||
| Raw and analyzed data | This paper | www.hudeca.com |
| Software and algorithms | ||
| Blender (v3.0) | Blender Foundation | https://www.blender.org/ |
| Handbrake (v1.6.1) | Handbrake | https://handbrake.fr/ |
| ImageJ (1.50e, Java 1.8.0_60, 64-bit) | NIH | http://imagej.nih.gov/ij/; RRID:SCR_003070 |
| Imaris x64 software suite (v9 to 10) | Oxford Instruments | https://imaris.oxinst.com/ |
| Imspector software for Blaze Ultramicroscope | Miltenyi | https://www.miltenyibiotec.com/FR-en/products/ultramicroscope-blaze.html |
| iMovie (v10.1.1) | Apple | http://www.apple.com/fr/imovie/ |
| Meshmixer (Version 3.5.474) | Autodesk | https://meshmixer.com/ |
| Meshlab (Version 2021.10) | Cignoni et al.91 | https://www.meshlab.net/# |
| Numpy (Version 1.22.3) | Harris et al.92 | https://numpy.org/ |
| Pandas (Version 1.4.2) | NumFOCUS, Inc. | https://pandas.pydata.org/ |
| Premiere Pro (2019) | Adobe | https://www.adobe.com |
| Pymeshlab (Version 2022.2.post4) | Cignoni et al.91 | https://www.meshlab.net/# |
| Syglass (v1.7.1 & 1.7.2) | IstoVisio, Inc. | https://www.syglass.io/ |
| TIFFFILE (Version 2022.3.25) | 10.5281/zenodo.8357648 | https://github.com/cgohlke/tifffile/ |
| Vedo (Version 2023.4.6) | 10.5281/zenodo.5330735 | https://vedo.embl.es/ |
| Verge3D (v3.9) | Soft8Soft | https://www.soft8soft.com/verge3d/ |
| Wavefront.OBJ (ImageJ plugin) | Virtual Insect Brain (VIB) Protocol | https://imagej.net/formats/wavefront-obj |
| Custom Python code: Mask_labels.ipynb | This paper | https://github.com/Megumi4952/Chedotal_Lab_Head_Development/Mask_labels.ipyn |
| Custom Python code 2: QECD_in_Folder.ipynb | This paper | https://github.com/Megumi4952/Chedotal_Lab_Head_Development/QECD_in_Folder.ipynb |
| Custom Python code 3: Merge_Meshes_for_3DP.ipynb | This paper | https://github.com/Megumi4952/Chedotal_Lab_Head_Development/Merge_Meshes_for_3DP.ipynb |
| Other | ||
| Resource website | Belle et al.19 | https://transparent-human-embryo.com/ |
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