resource source identifier antibodies rabbit monoclonal anti foxa2 cell signaling technology  (Cell Signaling Technology Inc)

Journal: Frontiers in Cell and Developmental Biology

Article Title: Efficient generation of human induced pluripotent stem cells from urine samples of patients with Fragile X syndrome

doi: 10.3389/fcell.2024.1489190

Figure Lengend Snippet: Antibodies used for the assessment of hiPSC pluripotency and functionality.

Article Snippet: FOXA2 , Cell Signaling Technology (#8186) , Endoderm marker , 1/400.

Techniques: Marker

Journal: Frontiers in Cell and Developmental Biology

Article Title: Efficient generation of human induced pluripotent stem cells from urine samples of patients with Fragile X syndrome

doi: 10.3389/fcell.2024.1489190

Figure Lengend Snippet: Markers used to validate the differentiation of embryonic lineages.

Article Snippet: FOXA2 , Cell Signaling Technology (#8186) , Endoderm marker , 1/400.

Techniques:

Journal: Frontiers in Cell and Developmental Biology

Article Title: Efficient generation of human induced pluripotent stem cells from urine samples of patients with Fragile X syndrome

doi: 10.3389/fcell.2024.1489190

Figure Lengend Snippet: Functional assessment of pluripotency via trilineage differentiation. Representative immunostainings of the ectodermal markers FOXA2 and SOX17 (A) , mesodermal markers Brachyury and NCAM (B) and ectodermal markers PAX6 and Nestin (C) in a control and FXS iPSC lines. Immunostaining of all iPSCs lines produced in this paper can be found in . Scale bar = 100 µm. (D) Quantification of lineage-specific markers expression in all iPSCs lines (n = 10 fields of views per cell line, mean ± SD).

Article Snippet: FOXA2 , Cell Signaling Technology (#8186) , Endoderm marker , 1/400.

Techniques: Functional Assay, Control, Immunostaining, Produced, Expressing

Journal: Developmental cell

Article Title: Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition.

doi: 10.1016/j.devcel.2024.04.021

Figure Lengend Snippet: Figure 2. Statistical analysis and tracking of live cluster dynamics reveal cluster competition during self-organization (A) Schematic of double reporter generation. Venus was knocked in after the 3rd exon at the C terminus of the endogenous FoxA2 locus, generating a fusion protein. In addition, an H2A-mCherry construct was knocked into the ubiquitously expressed Rosa26 locus to mark nuclei.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal rabbit anti-FOXA2 Cell Signalling Technologies Cat# 8186; RRID:AB_10891055 Polyclonal goat anti-FOXA2 R&D Cat# AF2400; RRID:AB_2294104 Monoclonal rabbit anti-SHH Cell Signalling Technologies Cat# 2207; RRID:AB_2188191 Monoclonal mouse anti-NKX6.1 DSHB Cat# F55A10; RRID:AB_532378 Monoclonal rabbit anti-LEF1 Cell Signalling Technologies Cat# 2230; RRID:AB_823558 Monoclonal rabbit anti-Phospho-SMAD1 (Ser463/465)/ SMAD5 (Ser463/465)/ SMAD9 (Ser465/467) Cell Signalling Technology Cat# 13820; RRID:AB_2493181 Monoclonal rabbit anti-Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) Cell Signalling Technology Cat# 4370; RRID:AB_2315112 Monoclonal rabbit anti-E-Cadherin Cell Signalling Technology Cat# 3195; RRID:AB_2291471 Monoclonal rat anti-N-Cadherin DSHB Cat# MNCD2; RRID:AB_528119 Monoclonal mouse anti-ß-Tubulin MPI-CBG N/A Alexa Fluor conjugated secondary antibodies for IHC (Donkey anti-Mouse/Goat/Rabbit) Invitrogen N/A HRP conjugated secondary antibodies for WB (Goat anti-Rabbit/Mouse) Invitrogen N/A DAPI Sigma-Aldrich Cat# D9542 Chemicals, peptides, and recombinant proteins N-2 Supplement (100X) Gibco Cat# 17502048 B-27 Supplement (50X), serum free Gibco Cat# 17504044 DMEM/F-12, no glutamine Gibco Cat# 21331020 Neurobasal Medium Gibco Cat# 21103049 L-Glutamine (200 mM) Gibco Cat# A2916801 2-Mercaptoethanol (50 mM) Gibco Cat# 31350010 Penicillin-Streptomycin Solution Gibco Cat# 15140130 CHIR 99021 Tocris Cat# 4423 PD 0325901 Tocris Cat# 4192 Mouse LIF Qkine Cat# Qk018-1000 Accutase Invitrogen Cat# 00-4555-56 Sodium Pyruvate (100 mM) Gibco Cat# 11360070 BMP4 R&D Cat# PHC9534 BMP7 R&D Cat# 354-GMP LDN-193189 Selleck Chemicals Cat# S2618 Noggin R&D Cat# 6057-NG-025 FGF2 PeproTech Cat# 100-18B FGF8b In house N/A IWP-2 Selleck Chemicals Cat# S7085 IWR-1endo Merck Cat# I0161 Gelatin Merck Cat# G2500 Puromycin -dihydrochlorid Thermo Scientific Cat# P9620 Neomycin Merck Cat# N1142 Geneticin (G418) Invivogen Cat# ant-gn-1 Trypsin-EDTA (0.25%) Gibco Cat# 25200056 Albumin (BSA) Fraction V (pH 7.0) Panreac AppliChem Cat# A1391 (Continued on next page) e1 Developmental Cell 59, 1940–1953.e1–e10, August 5, 2024

Techniques: Construct

Journal: Developmental cell

Article Title: Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition.

doi: 10.1016/j.devcel.2024.04.021

Figure Lengend Snippet: Figure 3. FOXA2+ cells express BMPs and Noggin, while FOXA2– cells display a higher pSMAD1/5/9 signal (A) Schematic of RNA-seq performed on sorted FOXA2+ and FOXA2 cell populations of day 5 NTOs made from the reporter cell line. (B) Activity plot of upstream regulators predicted to be activated or inhibited based on the observed expression changes in FOXA2+ versus FOXA2 cells. Regulators are colored based on activation Z score at a threshold of 1.8, and the top 20 candidates based on significance are labeled; an arrow next to a regulator name indicates significant up- or downregulation of the gene in FOXA2+ (versus FOXA2). (C) WNT, FGF, and BMP pathway members showing differential gene expression between FOXA2+ and FOXA2 cells. MA plot of the RNA-seq data showing log2 fold changes of genes over their average gene expression against samples (y axis: FOXA2+ versus FOXA2 log ratio values, x axis: log10(baseMean + 1) of average gene expression). Color highlights genes assigned to either WNT signaling pathway (GO: 0016055), FGF signaling pathway (GO: 0008543), or BMP signaling

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal rabbit anti-FOXA2 Cell Signalling Technologies Cat# 8186; RRID:AB_10891055 Polyclonal goat anti-FOXA2 R&D Cat# AF2400; RRID:AB_2294104 Monoclonal rabbit anti-SHH Cell Signalling Technologies Cat# 2207; RRID:AB_2188191 Monoclonal mouse anti-NKX6.1 DSHB Cat# F55A10; RRID:AB_532378 Monoclonal rabbit anti-LEF1 Cell Signalling Technologies Cat# 2230; RRID:AB_823558 Monoclonal rabbit anti-Phospho-SMAD1 (Ser463/465)/ SMAD5 (Ser463/465)/ SMAD9 (Ser465/467) Cell Signalling Technology Cat# 13820; RRID:AB_2493181 Monoclonal rabbit anti-Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) Cell Signalling Technology Cat# 4370; RRID:AB_2315112 Monoclonal rabbit anti-E-Cadherin Cell Signalling Technology Cat# 3195; RRID:AB_2291471 Monoclonal rat anti-N-Cadherin DSHB Cat# MNCD2; RRID:AB_528119 Monoclonal mouse anti-ß-Tubulin MPI-CBG N/A Alexa Fluor conjugated secondary antibodies for IHC (Donkey anti-Mouse/Goat/Rabbit) Invitrogen N/A HRP conjugated secondary antibodies for WB (Goat anti-Rabbit/Mouse) Invitrogen N/A DAPI Sigma-Aldrich Cat# D9542 Chemicals, peptides, and recombinant proteins N-2 Supplement (100X) Gibco Cat# 17502048 B-27 Supplement (50X), serum free Gibco Cat# 17504044 DMEM/F-12, no glutamine Gibco Cat# 21331020 Neurobasal Medium Gibco Cat# 21103049 L-Glutamine (200 mM) Gibco Cat# A2916801 2-Mercaptoethanol (50 mM) Gibco Cat# 31350010 Penicillin-Streptomycin Solution Gibco Cat# 15140130 CHIR 99021 Tocris Cat# 4423 PD 0325901 Tocris Cat# 4192 Mouse LIF Qkine Cat# Qk018-1000 Accutase Invitrogen Cat# 00-4555-56 Sodium Pyruvate (100 mM) Gibco Cat# 11360070 BMP4 R&D Cat# PHC9534 BMP7 R&D Cat# 354-GMP LDN-193189 Selleck Chemicals Cat# S2618 Noggin R&D Cat# 6057-NG-025 FGF2 PeproTech Cat# 100-18B FGF8b In house N/A IWP-2 Selleck Chemicals Cat# S7085 IWR-1endo Merck Cat# I0161 Gelatin Merck Cat# G2500 Puromycin -dihydrochlorid Thermo Scientific Cat# P9620 Neomycin Merck Cat# N1142 Geneticin (G418) Invivogen Cat# ant-gn-1 Trypsin-EDTA (0.25%) Gibco Cat# 25200056 Albumin (BSA) Fraction V (pH 7.0) Panreac AppliChem Cat# A1391 (Continued on next page) e1 Developmental Cell 59, 1940–1953.e1–e10, August 5, 2024

Techniques: RNA Sequencing, Activity Assay, Expressing, Activation Assay, Labeling, Gene Expression

Journal: Developmental cell

Article Title: Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition.

doi: 10.1016/j.devcel.2024.04.021

Figure Lengend Snippet: Figure 4. BMP pathway activation or suppression modulates FOXA2 cluster persistence (A) Timeline of BMP pathway perturbations using ‘‘large NTO’’ protocol relevant for (B)–(H) (see Figure S4). Perturbations were performed from days 4 to 6 after an 18 h RA pulse from days 2 to 3.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal rabbit anti-FOXA2 Cell Signalling Technologies Cat# 8186; RRID:AB_10891055 Polyclonal goat anti-FOXA2 R&D Cat# AF2400; RRID:AB_2294104 Monoclonal rabbit anti-SHH Cell Signalling Technologies Cat# 2207; RRID:AB_2188191 Monoclonal mouse anti-NKX6.1 DSHB Cat# F55A10; RRID:AB_532378 Monoclonal rabbit anti-LEF1 Cell Signalling Technologies Cat# 2230; RRID:AB_823558 Monoclonal rabbit anti-Phospho-SMAD1 (Ser463/465)/ SMAD5 (Ser463/465)/ SMAD9 (Ser465/467) Cell Signalling Technology Cat# 13820; RRID:AB_2493181 Monoclonal rabbit anti-Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) Cell Signalling Technology Cat# 4370; RRID:AB_2315112 Monoclonal rabbit anti-E-Cadherin Cell Signalling Technology Cat# 3195; RRID:AB_2291471 Monoclonal rat anti-N-Cadherin DSHB Cat# MNCD2; RRID:AB_528119 Monoclonal mouse anti-ß-Tubulin MPI-CBG N/A Alexa Fluor conjugated secondary antibodies for IHC (Donkey anti-Mouse/Goat/Rabbit) Invitrogen N/A HRP conjugated secondary antibodies for WB (Goat anti-Rabbit/Mouse) Invitrogen N/A DAPI Sigma-Aldrich Cat# D9542 Chemicals, peptides, and recombinant proteins N-2 Supplement (100X) Gibco Cat# 17502048 B-27 Supplement (50X), serum free Gibco Cat# 17504044 DMEM/F-12, no glutamine Gibco Cat# 21331020 Neurobasal Medium Gibco Cat# 21103049 L-Glutamine (200 mM) Gibco Cat# A2916801 2-Mercaptoethanol (50 mM) Gibco Cat# 31350010 Penicillin-Streptomycin Solution Gibco Cat# 15140130 CHIR 99021 Tocris Cat# 4423 PD 0325901 Tocris Cat# 4192 Mouse LIF Qkine Cat# Qk018-1000 Accutase Invitrogen Cat# 00-4555-56 Sodium Pyruvate (100 mM) Gibco Cat# 11360070 BMP4 R&D Cat# PHC9534 BMP7 R&D Cat# 354-GMP LDN-193189 Selleck Chemicals Cat# S2618 Noggin R&D Cat# 6057-NG-025 FGF2 PeproTech Cat# 100-18B FGF8b In house N/A IWP-2 Selleck Chemicals Cat# S7085 IWR-1endo Merck Cat# I0161 Gelatin Merck Cat# G2500 Puromycin -dihydrochlorid Thermo Scientific Cat# P9620 Neomycin Merck Cat# N1142 Geneticin (G418) Invivogen Cat# ant-gn-1 Trypsin-EDTA (0.25%) Gibco Cat# 25200056 Albumin (BSA) Fraction V (pH 7.0) Panreac AppliChem Cat# A1391 (Continued on next page) e1 Developmental Cell 59, 1940–1953.e1–e10, August 5, 2024

Techniques: Activation Assay

Journal: Developmental cell

Article Title: Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition.

doi: 10.1016/j.devcel.2024.04.021

Figure Lengend Snippet: Figure 5. In vivo role of NOGGIN in anterior floorplate size in the mouse embryo (A) Schematic of mouse crossing performed for inducible deletion of Noggin. E10.5 mouse showing the anatomy and section planes of the harvested and analyzed embryos. (B) Representative images of E10.5 control (NogFl/+;Sox2+/+ or NogFl/Fl;Sox2+/+) and Nog cKO (NogFl/Fl;Sox2CreERT2/+) embryos of mid/hindbrain (M/HB), cervical spinal cord (CSC), and thorax (THR) regions stained for DAPI (blue), FOXA2 (green), and SHH (magenta). Scale bars, 100 mm. (C) Normalized area of FOXA2 and SHH at different anterior-posterior levels of the embryonic NT. Quantification was made on serial sections of 6 control embryos (136 sections total, 33 for M/HB, 62 for CSC, 33 for THR) in purple and 3 Nog cKO embryos (68 sections total, 23 for M/HB, 30 for CSC, 15 for THR) in cyan from two litters. Kruskal-Wallis test and Dunn’s multiple comparison tests were performed between anatomical regions of control versus Nog cKO (FOXA2: M/HB versus M/HB p = 0.0165, CSC versus CSC p = 0.2706, THR versus THR p = 0.3926, SHH: M/HB versus M/HB p = 0.0031, CSC versus CSC p = 0.0792, THR versus THR p = 0.4484). Horizontal bars represent means of the data, asterisks indicate statistical significance, n.s. indicates non-significance.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal rabbit anti-FOXA2 Cell Signalling Technologies Cat# 8186; RRID:AB_10891055 Polyclonal goat anti-FOXA2 R&D Cat# AF2400; RRID:AB_2294104 Monoclonal rabbit anti-SHH Cell Signalling Technologies Cat# 2207; RRID:AB_2188191 Monoclonal mouse anti-NKX6.1 DSHB Cat# F55A10; RRID:AB_532378 Monoclonal rabbit anti-LEF1 Cell Signalling Technologies Cat# 2230; RRID:AB_823558 Monoclonal rabbit anti-Phospho-SMAD1 (Ser463/465)/ SMAD5 (Ser463/465)/ SMAD9 (Ser465/467) Cell Signalling Technology Cat# 13820; RRID:AB_2493181 Monoclonal rabbit anti-Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) Cell Signalling Technology Cat# 4370; RRID:AB_2315112 Monoclonal rabbit anti-E-Cadherin Cell Signalling Technology Cat# 3195; RRID:AB_2291471 Monoclonal rat anti-N-Cadherin DSHB Cat# MNCD2; RRID:AB_528119 Monoclonal mouse anti-ß-Tubulin MPI-CBG N/A Alexa Fluor conjugated secondary antibodies for IHC (Donkey anti-Mouse/Goat/Rabbit) Invitrogen N/A HRP conjugated secondary antibodies for WB (Goat anti-Rabbit/Mouse) Invitrogen N/A DAPI Sigma-Aldrich Cat# D9542 Chemicals, peptides, and recombinant proteins N-2 Supplement (100X) Gibco Cat# 17502048 B-27 Supplement (50X), serum free Gibco Cat# 17504044 DMEM/F-12, no glutamine Gibco Cat# 21331020 Neurobasal Medium Gibco Cat# 21103049 L-Glutamine (200 mM) Gibco Cat# A2916801 2-Mercaptoethanol (50 mM) Gibco Cat# 31350010 Penicillin-Streptomycin Solution Gibco Cat# 15140130 CHIR 99021 Tocris Cat# 4423 PD 0325901 Tocris Cat# 4192 Mouse LIF Qkine Cat# Qk018-1000 Accutase Invitrogen Cat# 00-4555-56 Sodium Pyruvate (100 mM) Gibco Cat# 11360070 BMP4 R&D Cat# PHC9534 BMP7 R&D Cat# 354-GMP LDN-193189 Selleck Chemicals Cat# S2618 Noggin R&D Cat# 6057-NG-025 FGF2 PeproTech Cat# 100-18B FGF8b In house N/A IWP-2 Selleck Chemicals Cat# S7085 IWR-1endo Merck Cat# I0161 Gelatin Merck Cat# G2500 Puromycin -dihydrochlorid Thermo Scientific Cat# P9620 Neomycin Merck Cat# N1142 Geneticin (G418) Invivogen Cat# ant-gn-1 Trypsin-EDTA (0.25%) Gibco Cat# 25200056 Albumin (BSA) Fraction V (pH 7.0) Panreac AppliChem Cat# A1391 (Continued on next page) e1 Developmental Cell 59, 1940–1953.e1–e10, August 5, 2024

Techniques: In Vivo, Control, Staining, Comparison