Recombinant:Article Title: Molecular profiling of human blastocysts reveals primitive endoderm defects among embryos of decreased implantation potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-human monoclonal CDX2 antibody Abcam Cat# ab76541; RRID:AB_1523334 Mouse anti-human monoclonal NANOG antibody Millipore Cat# MABD24; RRID:AB_11203826 Rat anti-human monoclonal GATA4 antibody Invitrogen Cat# 14-9980-80 Goat anti-human polyclonal GATA6 antibody R&D Systems Cat# AF1700; RRID:AB_2108901 Alexa Fluor 555 highly cross-adsorbed conjugated donkey anti-rabbit IgG (H+L) secondary antibody Thermo Fisher Scientific Cat# A-31572; RRID:AB_162543 Alexa Fluor 488 conjugated donkey anti-rat IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-21208; RRID:AB_2535794 Alexa Fluor 647 conjugated donkey anti-mouse IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-31571 DAPI Solution Novus Biologicals Cat# NBP2-31156 Biological samples Good and poor morphology human blastocysts Reproductive Partners Fertility Center IRB Project 191494 Chemicals, peptides, and recombinant proteins G1-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/ G2-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/g-2/ G-PGD media Vitrolife https://www.vitrolife.com/globalassets/ support-documents/safety-data-sheets/ sds_g_pgd.pdf Acid Tyrode’s solution Sigma T1788 Paraformaldehyde Electron Microscopy Sciences 15710 Tween-20 Fisher BP337 Critical commercial assays PGT-A: ArrayCGH Reprogenetics N/A (performed by source) PGT-A: NGS Igenomics N/A (performed by source) SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888 Nextera XT DNA library preparation kit Illumina FC-131-1024 Deposited data Raw and analyzed data This paper GEO: GSE136106 Software and algorithms STAR (2.5.2a) Dobin et al.81,82 https://github.com/alexdobin/STAR cutadapt (v1.10) Martin et al.83 https://cutadapt.readthedocs.io/ en/stable/ samtools Li et al.84 https://samtools.sourceforge.net/ FeatureCounts (Subread) (release 1.5.2) Liao et al.85 https://subread.sourceforge.net/ edgeR Robinson et al.86,87 https://bioconductor.org/packages/ release/bioc/html/edgeR.html DESeq2 Love et al.88 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham et al.89 https://cran.r-project.org/web/ packages/ggplot2/citation.html CIBERSORT Newman et al.43 https://cibersortx.stanford.edu/ (Continued on next page) Cell Reports 43, 113701, February 27, 2024 17 ..
Electron Microscopy:Article Title: Molecular profiling of human blastocysts reveals primitive endoderm defects among embryos of decreased implantation potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-human monoclonal CDX2 antibody Abcam Cat# ab76541; RRID:AB_1523334 Mouse anti-human monoclonal NANOG antibody Millipore Cat# MABD24; RRID:AB_11203826 Rat anti-human monoclonal GATA4 antibody Invitrogen Cat# 14-9980-80 Goat anti-human polyclonal GATA6 antibody R&D Systems Cat# AF1700; RRID:AB_2108901 Alexa Fluor 555 highly cross-adsorbed conjugated donkey anti-rabbit IgG (H+L) secondary antibody Thermo Fisher Scientific Cat# A-31572; RRID:AB_162543 Alexa Fluor 488 conjugated donkey anti-rat IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-21208; RRID:AB_2535794 Alexa Fluor 647 conjugated donkey anti-mouse IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-31571 DAPI Solution Novus Biologicals Cat# NBP2-31156 Biological samples Good and poor morphology human blastocysts Reproductive Partners Fertility Center IRB Project 191494 Chemicals, peptides, and recombinant proteins G1-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/ G2-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/g-2/ G-PGD media Vitrolife https://www.vitrolife.com/globalassets/ support-documents/safety-data-sheets/ sds_g_pgd.pdf Acid Tyrode’s solution Sigma T1788 Paraformaldehyde Electron Microscopy Sciences 15710 Tween-20 Fisher BP337 Critical commercial assays PGT-A: ArrayCGH Reprogenetics N/A (performed by source) PGT-A: NGS Igenomics N/A (performed by source) SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888 Nextera XT DNA library preparation kit Illumina FC-131-1024 Deposited data Raw and analyzed data This paper GEO: GSE136106 Software and algorithms STAR (2.5.2a) Dobin et al.81,82 https://github.com/alexdobin/STAR cutadapt (v1.10) Martin et al.83 https://cutadapt.readthedocs.io/ en/stable/ samtools Li et al.84 https://samtools.sourceforge.net/ FeatureCounts (Subread) (release 1.5.2) Liao et al.85 https://subread.sourceforge.net/ edgeR Robinson et al.86,87 https://bioconductor.org/packages/ release/bioc/html/edgeR.html DESeq2 Love et al.88 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham et al.89 https://cran.r-project.org/web/ packages/ggplot2/citation.html CIBERSORT Newman et al.43 https://cibersortx.stanford.edu/ (Continued on next page) Cell Reports 43, 113701, February 27, 2024 17 ..
Next-Generation Sequencing:Article Title: Molecular profiling of human blastocysts reveals primitive endoderm defects among embryos of decreased implantation potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-human monoclonal CDX2 antibody Abcam Cat# ab76541; RRID:AB_1523334 Mouse anti-human monoclonal NANOG antibody Millipore Cat# MABD24; RRID:AB_11203826 Rat anti-human monoclonal GATA4 antibody Invitrogen Cat# 14-9980-80 Goat anti-human polyclonal GATA6 antibody R&D Systems Cat# AF1700; RRID:AB_2108901 Alexa Fluor 555 highly cross-adsorbed conjugated donkey anti-rabbit IgG (H+L) secondary antibody Thermo Fisher Scientific Cat# A-31572; RRID:AB_162543 Alexa Fluor 488 conjugated donkey anti-rat IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-21208; RRID:AB_2535794 Alexa Fluor 647 conjugated donkey anti-mouse IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-31571 DAPI Solution Novus Biologicals Cat# NBP2-31156 Biological samples Good and poor morphology human blastocysts Reproductive Partners Fertility Center IRB Project 191494 Chemicals, peptides, and recombinant proteins G1-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/ G2-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/g-2/ G-PGD media Vitrolife https://www.vitrolife.com/globalassets/ support-documents/safety-data-sheets/ sds_g_pgd.pdf Acid Tyrode’s solution Sigma T1788 Paraformaldehyde Electron Microscopy Sciences 15710 Tween-20 Fisher BP337 Critical commercial assays PGT-A: ArrayCGH Reprogenetics N/A (performed by source) PGT-A: NGS Igenomics N/A (performed by source) SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888 Nextera XT DNA library preparation kit Illumina FC-131-1024 Deposited data Raw and analyzed data This paper GEO: GSE136106 Software and algorithms STAR (2.5.2a) Dobin et al.81,82 https://github.com/alexdobin/STAR cutadapt (v1.10) Martin et al.83 https://cutadapt.readthedocs.io/ en/stable/ samtools Li et al.84 https://samtools.sourceforge.net/ FeatureCounts (Subread) (release 1.5.2) Liao et al.85 https://subread.sourceforge.net/ edgeR Robinson et al.86,87 https://bioconductor.org/packages/ release/bioc/html/edgeR.html DESeq2 Love et al.88 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham et al.89 https://cran.r-project.org/web/ packages/ggplot2/citation.html CIBERSORT Newman et al.43 https://cibersortx.stanford.edu/ (Continued on next page) Cell Reports 43, 113701, February 27, 2024 17 ..
Sequencing:Article Title: Molecular profiling of human blastocysts reveals primitive endoderm defects among embryos of decreased implantation potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-human monoclonal CDX2 antibody Abcam Cat# ab76541; RRID:AB_1523334 Mouse anti-human monoclonal NANOG antibody Millipore Cat# MABD24; RRID:AB_11203826 Rat anti-human monoclonal GATA4 antibody Invitrogen Cat# 14-9980-80 Goat anti-human polyclonal GATA6 antibody R&D Systems Cat# AF1700; RRID:AB_2108901 Alexa Fluor 555 highly cross-adsorbed conjugated donkey anti-rabbit IgG (H+L) secondary antibody Thermo Fisher Scientific Cat# A-31572; RRID:AB_162543 Alexa Fluor 488 conjugated donkey anti-rat IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-21208; RRID:AB_2535794 Alexa Fluor 647 conjugated donkey anti-mouse IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-31571 DAPI Solution Novus Biologicals Cat# NBP2-31156 Biological samples Good and poor morphology human blastocysts Reproductive Partners Fertility Center IRB Project 191494 Chemicals, peptides, and recombinant proteins G1-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/ G2-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/g-2/ G-PGD media Vitrolife https://www.vitrolife.com/globalassets/ support-documents/safety-data-sheets/ sds_g_pgd.pdf Acid Tyrode’s solution Sigma T1788 Paraformaldehyde Electron Microscopy Sciences 15710 Tween-20 Fisher BP337 Critical commercial assays PGT-A: ArrayCGH Reprogenetics N/A (performed by source) PGT-A: NGS Igenomics N/A (performed by source) SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888 Nextera XT DNA library preparation kit Illumina FC-131-1024 Deposited data Raw and analyzed data This paper GEO: GSE136106 Software and algorithms STAR (2.5.2a) Dobin et al.81,82 https://github.com/alexdobin/STAR cutadapt (v1.10) Martin et al.83 https://cutadapt.readthedocs.io/ en/stable/ samtools Li et al.84 https://samtools.sourceforge.net/ FeatureCounts (Subread) (release 1.5.2) Liao et al.85 https://subread.sourceforge.net/ edgeR Robinson et al.86,87 https://bioconductor.org/packages/ release/bioc/html/edgeR.html DESeq2 Love et al.88 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham et al.89 https://cran.r-project.org/web/ packages/ggplot2/citation.html CIBERSORT Newman et al.43 https://cibersortx.stanford.edu/ (Continued on next page) Cell Reports 43, 113701, February 27, 2024 17 ..
DNA Library Preparation:Article Title: Molecular profiling of human blastocysts reveals primitive endoderm defects among embryos of decreased implantation potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-human monoclonal CDX2 antibody Abcam Cat# ab76541; RRID:AB_1523334 Mouse anti-human monoclonal NANOG antibody Millipore Cat# MABD24; RRID:AB_11203826 Rat anti-human monoclonal GATA4 antibody Invitrogen Cat# 14-9980-80 Goat anti-human polyclonal GATA6 antibody R&D Systems Cat# AF1700; RRID:AB_2108901 Alexa Fluor 555 highly cross-adsorbed conjugated donkey anti-rabbit IgG (H+L) secondary antibody Thermo Fisher Scientific Cat# A-31572; RRID:AB_162543 Alexa Fluor 488 conjugated donkey anti-rat IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-21208; RRID:AB_2535794 Alexa Fluor 647 conjugated donkey anti-mouse IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-31571 DAPI Solution Novus Biologicals Cat# NBP2-31156 Biological samples Good and poor morphology human blastocysts Reproductive Partners Fertility Center IRB Project 191494 Chemicals, peptides, and recombinant proteins G1-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/ G2-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/g-2/ G-PGD media Vitrolife https://www.vitrolife.com/globalassets/ support-documents/safety-data-sheets/ sds_g_pgd.pdf Acid Tyrode’s solution Sigma T1788 Paraformaldehyde Electron Microscopy Sciences 15710 Tween-20 Fisher BP337 Critical commercial assays PGT-A: ArrayCGH Reprogenetics N/A (performed by source) PGT-A: NGS Igenomics N/A (performed by source) SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888 Nextera XT DNA library preparation kit Illumina FC-131-1024 Deposited data Raw and analyzed data This paper GEO: GSE136106 Software and algorithms STAR (2.5.2a) Dobin et al.81,82 https://github.com/alexdobin/STAR cutadapt (v1.10) Martin et al.83 https://cutadapt.readthedocs.io/ en/stable/ samtools Li et al.84 https://samtools.sourceforge.net/ FeatureCounts (Subread) (release 1.5.2) Liao et al.85 https://subread.sourceforge.net/ edgeR Robinson et al.86,87 https://bioconductor.org/packages/ release/bioc/html/edgeR.html DESeq2 Love et al.88 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham et al.89 https://cran.r-project.org/web/ packages/ggplot2/citation.html CIBERSORT Newman et al.43 https://cibersortx.stanford.edu/ (Continued on next page) Cell Reports 43, 113701, February 27, 2024 17 ..
Software:Article Title: Molecular profiling of human blastocysts reveals primitive endoderm defects among embryos of decreased implantation potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-human monoclonal CDX2 antibody Abcam Cat# ab76541; RRID:AB_1523334 Mouse anti-human monoclonal NANOG antibody Millipore Cat# MABD24; RRID:AB_11203826 Rat anti-human monoclonal GATA4 antibody Invitrogen Cat# 14-9980-80 Goat anti-human polyclonal GATA6 antibody R&D Systems Cat# AF1700; RRID:AB_2108901 Alexa Fluor 555 highly cross-adsorbed conjugated donkey anti-rabbit IgG (H+L) secondary antibody Thermo Fisher Scientific Cat# A-31572; RRID:AB_162543 Alexa Fluor 488 conjugated donkey anti-rat IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-21208; RRID:AB_2535794 Alexa Fluor 647 conjugated donkey anti-mouse IgG (H+L) Highly Cross-Adsorbed secondary antibody Thermo Fisher Scientific Cat# A-31571 DAPI Solution Novus Biologicals Cat# NBP2-31156 Biological samples Good and poor morphology human blastocysts Reproductive Partners Fertility Center IRB Project 191494 Chemicals, peptides, and recombinant proteins G1-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/ G2-PLUS media Vitrolife https://www.vitrolife.com/products/ ivf-media–oil/g-2/ G-PGD media Vitrolife https://www.vitrolife.com/globalassets/ support-documents/safety-data-sheets/ sds_g_pgd.pdf Acid Tyrode’s solution Sigma T1788 Paraformaldehyde Electron Microscopy Sciences 15710 Tween-20 Fisher BP337 Critical commercial assays PGT-A: ArrayCGH Reprogenetics N/A (performed by source) PGT-A: NGS Igenomics N/A (performed by source) SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing Clontech 634888 Nextera XT DNA library preparation kit Illumina FC-131-1024 Deposited data Raw and analyzed data This paper GEO: GSE136106 Software and algorithms STAR (2.5.2a) Dobin et al.81,82 https://github.com/alexdobin/STAR cutadapt (v1.10) Martin et al.83 https://cutadapt.readthedocs.io/ en/stable/ samtools Li et al.84 https://samtools.sourceforge.net/ FeatureCounts (Subread) (release 1.5.2) Liao et al.85 https://subread.sourceforge.net/ edgeR Robinson et al.86,87 https://bioconductor.org/packages/ release/bioc/html/edgeR.html DESeq2 Love et al.88 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham et al.89 https://cran.r-project.org/web/ packages/ggplot2/citation.html CIBERSORT Newman et al.43 https://cibersortx.stanford.edu/ (Continued on next page) Cell Reports 43, 113701, February 27, 2024 17 ..
Incubation:Article Title: Formation of memory assemblies through the DNA-sensing TLR9 pathway
Article Snippet: For C1 probe TSA Vivid Fluorophore Kit 520 (Biotechne, 7523) was used, for C2 and C3, positive and negative probes TSA Vivid Fluorophore Kit 650 (7527) was used. .. Sections were incubated with goat anti-rabbit Alexa-568 secondary antibody (1:300, Invitrogen, A11036) and DAPI solution (ACD bio), and mounted with Prolong Gold Antifade Mountant (ThermoFisher Scientific, 33342). .. Images were acquired with an Andor BC43 spinning disk confocal microscope (Oxford Instruments) controlled by the Fusion software from Andor, using a 10× air 0.45 NA objective, a 60× oil immersion 1.42 NA objective, a CMOS camera (6.5 μm pixel; 2,048 × 2,000 pixels generating 16-bit, monochrome images) with no binning.
other:Article Title: Altered Fhod3 expression involved in progressive high-frequency hearing loss via dysregulation of actin polymerization stoichiometry in the cuticular plate
Article Snippet: The following antibodies were used (polyclonal unless indicated): Fhod3 (Thermo Fisher Scientific, Cat# PA5-23313, 1:100); Myo6 (Proteus Bioscience, Cat# 25–6791, 1:250); anti-HA tag (Abcam, Cat# ab9110, 1:100); TuJ-1 monoclonal (R&D systems, Cat# MAB1195, 1:500); Alexa Fluor 568 conjugated phalloidin (Thermo Fischer Scientific, A12380, 1:250); 4’6369 diamidino-2-phenylindole (DAPI) (Novus Biologicals, Cat# NBP2-31156, 1:50,000); Alexa Fluor 647-conjugated anti-mouse IgG2a (Thermo Fischer Scientific, Cat# A-21241, 1:500); Alexa Fluor 371 488-conjugated anti-rabbit IgG (Themo Fischer Scientific, Cat# A-11008, 1:500).
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