Cell Culture:Article Title: Suppression of ferroptosis by vitamin A or radical-trapping antioxidants is essential for neuronal development
Article Snippet: From day 5 to 10, cells were cultured in the presence of TGFβ and BMP inhibitors (LDN193189, #72142, Stem Cell Technologies; SB431542, #1614, Tocris) to trigger cortical precursors for cortical neuron differentiation. .. From day 10 to 20, the cells were cultured in Neurobasal media (#21103-049, ThermoFisher Scientific) and DMEM F-12 media (#11330-032/ Thermo Fisher Scientific) supplemented with L-Glutamine (#25030-024, Thermo Fisher Scientific), B27(-vitamin A) (#12587010, Thermo Fisher Scientific), N2 supplement B (# 07156, StemCell Technologies), D-(+) Glucose, 2-mercaptoethanol, Sodium bicarbonate and Progesterone. .. From day 20 cortical neurons were cultured on polyornithine (PO)/ laminin (L)/fibronectin (FN) coated wells and kept in neuronal differentiation media (Neurobasal media (#21103-049, Thermo Fisher Scientific), 1% Pen/Strep (#15140-122, Thermo Fisher Scientific), L-Glutamine, B27(-vitamin A) supplemented with DAPT (#2634, Tocris) until day 30.
Expressing:Article Title: Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits.
Article Snippet: .. Astrocytes were differentiated from the UCSFi001-A line (human pluripotent stem cells from healthy male donor) expressing dCas9-KRAB following our previously published protocol.55 Specifically, on day 0, hPSCs were differentiated in N2 medium [500 mL DMEM/F12 (1:1) (Gibco, Cat # 11320-033), 5 mL Glutamax (Gibco, Cat # 35050-061), 7.5 mL Sucrose (20%, SIGMA, Cat # S0389), 5 mL N2 supplement B (StemCell Technologies, Cat # 07156)] supplemented with SB431542 (10 mM, Tocris, Cat # 1614), XAV939 (2 mM, Stemgent, Cat # 04-00046) and LDN-193189 (100 nM, Stemgent, Cat # 04-0074) along with doxycycline hyclate (2 mg.mL-1, Sigma, Cat # D9891) with Y27632 (5 mM, Stemgent, Cat # 04-0012), at 37C. .. Day 1 was a step-down of small molecules, where N2 medium was supplemented with SB431542 (5 mM), XAV939 (1 mM) and LDN-193189 (50 nM) with doxycycline hyclate (2 mg.mL-1) and Zeocin (1 mg.mL-1, Invitrogen, Cat # 46-059).
Virus:Article Title: Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AF488-anti TLR4 Invitrogen 53-9917-42, lot2562921; RRID: AB_1963634 AF488-nti CD14 Invitrogen 53-0149-42, lot 2869688; RRID: AB_2744748 Anti IRAK1 Invitrogen MA5-15783, lotzd4273851; RRID: AB_11154024 AF488-anti mouse Invitrogen A32723, lot yl386289; RRID: AB_2633275 BV421 anti-human CD45, clone 2D1 Biolegend Cat# 368522; RRID: AB_2687375 FITC anti-human CD3, clone OKT3 Biolegend Cat# 317306; RRID: AB_571907 Bacterial and virus strains Stbl3 bacteria Invitrogen C7373-03 Biological Samples LRS Cone Stemcell technology Catalog # 200-0093 Chemicals, peptides, and recombinant proteins N2 supplement B StemCell Technologies 07156 SB431542 Stemgent 1614 XAV939 Stemgent 04-00046 LDN-193189 Stemgent 04-0074 Y27632 Stemgent 04-0012 TransIT-LT1 Mirus MIR 2304 polybrene Millipore sigma TR-1003-G puromycine Gibco A11138-03 blasticidin Gibco A11139-03 lps Sigma Aldrich L4516-1MG phorbol-12-myristate-13-acetate Sigma Aldrich P8139-1MG Megascript T7 transcription kit Thermofisher AM1334 ethylene carbonate Sigma aldrich E26258-500g fiducial beads Polysciences 17149- 10 deionized formamide J.T.Baker 4028-01 40% acrylamide/bis-acrylamide 19:1 Bio-Rad 1610144 Trolox Millipore sigma 238813-5g protocatechuic acid Sigma Aldrich 37580 recombinant protocatechuate 3,4-dioxygenase Oriental yeast co, ltd 46852004 TCEP Thermo scientific 77720 ammonium persulfate Sigma aldrich 09913-100mg yeast tRNA Invitrogen Am7119 dextran sulfate, 50% solution Millipore sigma S4030 acetic acid, glacial J.T. .. Baker 64-19-7 N,N,N,N’- Tetramethyl-ethylenediamine (TEMED) Sigma aldrich T9281-50mL proteinase K NEB P8107s RNAse inhibitor, murine NEB M0314L Proteinase K NEB T2010S RNA miniprep kit Monarch T2010s Fura-4AM Thermofisher scientific F14201 Matrigel (Growth Factor Reduced) Corning cat # 356239 Ficoll Paque Plus Cytiva cat # 17-1440-02 ACK lysing buffer Gibco cat # A1049201 (Continued on next page) ll OPEN ACCESS Cell 188, 1–18.e1–e8, April 17, 2025 e1 Please cite this article in press as: Binan et al., Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits, Cell (2025), https://doi.org/10.1016/j.cell.2025.02.012 Article
Bacteria:Article Title: Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AF488-anti TLR4 Invitrogen 53-9917-42, lot2562921; RRID: AB_1963634 AF488-nti CD14 Invitrogen 53-0149-42, lot 2869688; RRID: AB_2744748 Anti IRAK1 Invitrogen MA5-15783, lotzd4273851; RRID: AB_11154024 AF488-anti mouse Invitrogen A32723, lot yl386289; RRID: AB_2633275 BV421 anti-human CD45, clone 2D1 Biolegend Cat# 368522; RRID: AB_2687375 FITC anti-human CD3, clone OKT3 Biolegend Cat# 317306; RRID: AB_571907 Bacterial and virus strains Stbl3 bacteria Invitrogen C7373-03 Biological Samples LRS Cone Stemcell technology Catalog # 200-0093 Chemicals, peptides, and recombinant proteins N2 supplement B StemCell Technologies 07156 SB431542 Stemgent 1614 XAV939 Stemgent 04-00046 LDN-193189 Stemgent 04-0074 Y27632 Stemgent 04-0012 TransIT-LT1 Mirus MIR 2304 polybrene Millipore sigma TR-1003-G puromycine Gibco A11138-03 blasticidin Gibco A11139-03 lps Sigma Aldrich L4516-1MG phorbol-12-myristate-13-acetate Sigma Aldrich P8139-1MG Megascript T7 transcription kit Thermofisher AM1334 ethylene carbonate Sigma aldrich E26258-500g fiducial beads Polysciences 17149- 10 deionized formamide J.T.Baker 4028-01 40% acrylamide/bis-acrylamide 19:1 Bio-Rad 1610144 Trolox Millipore sigma 238813-5g protocatechuic acid Sigma Aldrich 37580 recombinant protocatechuate 3,4-dioxygenase Oriental yeast co, ltd 46852004 TCEP Thermo scientific 77720 ammonium persulfate Sigma aldrich 09913-100mg yeast tRNA Invitrogen Am7119 dextran sulfate, 50% solution Millipore sigma S4030 acetic acid, glacial J.T. .. Baker 64-19-7 N,N,N,N’- Tetramethyl-ethylenediamine (TEMED) Sigma aldrich T9281-50mL proteinase K NEB P8107s RNAse inhibitor, murine NEB M0314L Proteinase K NEB T2010S RNA miniprep kit Monarch T2010s Fura-4AM Thermofisher scientific F14201 Matrigel (Growth Factor Reduced) Corning cat # 356239 Ficoll Paque Plus Cytiva cat # 17-1440-02 ACK lysing buffer Gibco cat # A1049201 (Continued on next page) ll OPEN ACCESS Cell 188, 1–18.e1–e8, April 17, 2025 e1 Please cite this article in press as: Binan et al., Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits, Cell (2025), https://doi.org/10.1016/j.cell.2025.02.012 Article
Recombinant:Article Title: Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies AF488-anti TLR4 Invitrogen 53-9917-42, lot2562921; RRID: AB_1963634 AF488-nti CD14 Invitrogen 53-0149-42, lot 2869688; RRID: AB_2744748 Anti IRAK1 Invitrogen MA5-15783, lotzd4273851; RRID: AB_11154024 AF488-anti mouse Invitrogen A32723, lot yl386289; RRID: AB_2633275 BV421 anti-human CD45, clone 2D1 Biolegend Cat# 368522; RRID: AB_2687375 FITC anti-human CD3, clone OKT3 Biolegend Cat# 317306; RRID: AB_571907 Bacterial and virus strains Stbl3 bacteria Invitrogen C7373-03 Biological Samples LRS Cone Stemcell technology Catalog # 200-0093 Chemicals, peptides, and recombinant proteins N2 supplement B StemCell Technologies 07156 SB431542 Stemgent 1614 XAV939 Stemgent 04-00046 LDN-193189 Stemgent 04-0074 Y27632 Stemgent 04-0012 TransIT-LT1 Mirus MIR 2304 polybrene Millipore sigma TR-1003-G puromycine Gibco A11138-03 blasticidin Gibco A11139-03 lps Sigma Aldrich L4516-1MG phorbol-12-myristate-13-acetate Sigma Aldrich P8139-1MG Megascript T7 transcription kit Thermofisher AM1334 ethylene carbonate Sigma aldrich E26258-500g fiducial beads Polysciences 17149- 10 deionized formamide J.T.Baker 4028-01 40% acrylamide/bis-acrylamide 19:1 Bio-Rad 1610144 Trolox Millipore sigma 238813-5g protocatechuic acid Sigma Aldrich 37580 recombinant protocatechuate 3,4-dioxygenase Oriental yeast co, ltd 46852004 TCEP Thermo scientific 77720 ammonium persulfate Sigma aldrich 09913-100mg yeast tRNA Invitrogen Am7119 dextran sulfate, 50% solution Millipore sigma S4030 acetic acid, glacial J.T. .. Baker 64-19-7 N,N,N,N’- Tetramethyl-ethylenediamine (TEMED) Sigma aldrich T9281-50mL proteinase K NEB P8107s RNAse inhibitor, murine NEB M0314L Proteinase K NEB T2010S RNA miniprep kit Monarch T2010s Fura-4AM Thermofisher scientific F14201 Matrigel (Growth Factor Reduced) Corning cat # 356239 Ficoll Paque Plus Cytiva cat # 17-1440-02 ACK lysing buffer Gibco cat # A1049201 (Continued on next page) ll OPEN ACCESS Cell 188, 1–18.e1–e8, April 17, 2025 e1 Please cite this article in press as: Binan et al., Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits, Cell (2025), https://doi.org/10.1016/j.cell.2025.02.012 Article
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