Sequencing:Article Title: Substantial genomic and methylation variability between MCF-7 sublines
Article Snippet: .. We note that as both samples have relatively similar coverage (x28 ATCC vs x30 ECACC), these differences are unlikely to arise from differences in sequencing coverage, which may influence methylation call accuracy ( ). .. From the phased data (Supplemental Table 2), the methylation distribution between the haplotypes of each subline showed the ECACC subline had substantially fewer allele-specific DMRs (435, areaStat > 1000, Supplemental Table 2a) compared to the ATCC subline (959, areaStat > 1000, Supplemental Table 2b), indicating the ATCC subline was more prone to haplotype-specific methylation alterations.
Methylation:Article Title: Substantial genomic and methylation variability between MCF-7 sublines
Article Snippet: .. We note that as both samples have relatively similar coverage (x28 ATCC vs x30 ECACC), these differences are unlikely to arise from differences in sequencing coverage, which may influence methylation call accuracy ( ). .. From the phased data (Supplemental Table 2), the methylation distribution between the haplotypes of each subline showed the ECACC subline had substantially fewer allele-specific DMRs (435, areaStat > 1000, Supplemental Table 2a) compared to the ATCC subline (959, areaStat > 1000, Supplemental Table 2b), indicating the ATCC subline was more prone to haplotype-specific methylation alterations.
Isolation:Article Title: HEV-Targeted Antibody-Drug Conjugate Promotes Long-Term Cardiac Allograft Acceptance
Article Snippet: .. The cells were then isolated with cell sorting.35 PNAd-positive CHO cells and CHO Lec2 cells (referred to as PNAd-negative cells)37 were cultured in F-12K medium (ATCC, Manassas, VA) with 10% FBS and 1% pen/strep. ..
Cell Culture:Article Title: HEV-Targeted Antibody-Drug Conjugate Promotes Long-Term Cardiac Allograft Acceptance
Article Snippet: .. The cells were then isolated with cell sorting.35 PNAd-positive CHO cells and CHO Lec2 cells (referred to as PNAd-negative cells)37 were cultured in F-12K medium (ATCC, Manassas, VA) with 10% FBS and 1% pen/strep. ..
Article Title: Mutated PIGGYBAC® transposase
Article Snippet: .. Cell culture media, which may be further supplemented with other components to maximize cell growth, cell viability, and/or recombinant protein production in a particular cultured host cell, are commercially available and include RPMI-1640 Medium, RPMI-1641 Medium, Dulbecco's Modified Eagle's Medium (DMEM), Minimum Essential Medium Eagle, F-12K Medium, Ham's F12 Medium, Iscove's Modified Dulbecco's Medium, McCoy's 5A Medium, Leibovitz's L-15 Medium, and serum-free media such as EX-CELLTM 300 Series, among others, which can be obtained from the American Type Culture Collection or SAFC Biosciences, as well as other vendors. ..
Article Title: Engineering vascularized 3D tissues: An optimized seeding protocol for collagen-based scaffolds
Article Snippet: .. Reagents/tools , Cell line and medium • Primary human umbilical vein endothelial cells, HUVECs (ATCC, Manasses, VA, cat # PCS–100–010) • Vascular cell basal medium (ATCC, cat # PCS–100–030) supplemented with endothelial cell growth kit-VEGF (ATCC, No. PCS–100–041) and 1 % penicillin/streptomycin (ThermoFisher, cat # 15,140,122) Equipment • PHCbi CO 2 Incubator • Countess 3 Automated Cell Counter (ThermoFisher Scientific) • NuWind Multi-Application Centrifuge • Leica TCS SP5 confocal microscope Reagents • Dulbecco’s phosphate-buffered saline (DPBS, ThermoFisher Scientific, cat # 14,040,182) • Trypsin-EDTA (ATCC, cat # 30–2101) • Cubic collagen-based Spongostan Dental MS0005 (Ethicon, Johnson & Johnson) • 4 % paraformaldehyde (PFA, Boster, cat # AR1068) • Phosphate buffered saline (PBS, ThermoFisher Scientific, cat # 10,010,023) • 1 % bovine serum albumin (BSA, Biophoretics, cat # BCZ11920.1 ) • Phalloidin (FITC, ThermoFisher Scientific, cat # F432) • 4′,6-diamidino-2-phenylindole (DAPI, Invitrogen, cat # D1306) Software • LAS AF software • ImageJ Angiogenesis Analysis • GraphPad Prism 10.5.0 Plasticware • T75 cm 2 cell culture flasks (VWR, cat # 10,062–860) • 15 ml conical centrifuge tubes (Oxford Lab Products, cat # OCT-15B) • 0.65 mL microcentrifuge tubes (VWR, cat # 87,003–290) • 12-well plates (VWR, cat # 10,861–556) • Scalpel handle #3 • Sterile surgical carbon steel blades (P&P Medical Surgical, size 10) • Tweezers • 20 μL sterile pipette tips (Oxford Lab Products, cat # XR-20-SLF) • 200 μL sterile pipette tips (Oxford Lab Products, cat # XR-200-SLF) • 1000 μL sterile pipette tips (Oxford Lab Products, cat # XR-1000-SLF) • 20 μL pipette (Eppendorf, cat # ES-20F) • 200 μL pipette (Eppendorf, cat # ES-200F) • 1000 μL pipette (Eppendorf, cat # ES-1000F) • 5 mL serological pipettes (Oxford Lab Products, cat # OSC-5C) • 10 mL serological pipettes (Oxford Lab Products, cat # OSP-10C). .. Experimental design , Endothelial cells were seeded in a commercial 3D collagen scaffold to achieve a vascular network. Scaffolded cells were dyed with DAPI and FITC to visualize branching, which was further quantified using ImageJ Angiogenesis Analysis. Scaffold saturation, cell density, one-sided and two-sided seeding, and incubation period were altered to determine the optimal method for achieving maximal vascularization and branching..
Recombinant:Article Title: Mutated PIGGYBAC® transposase
Article Snippet: .. Cell culture media, which may be further supplemented with other components to maximize cell growth, cell viability, and/or recombinant protein production in a particular cultured host cell, are commercially available and include RPMI-1640 Medium, RPMI-1641 Medium, Dulbecco's Modified Eagle's Medium (DMEM), Minimum Essential Medium Eagle, F-12K Medium, Ham's F12 Medium, Iscove's Modified Dulbecco's Medium, McCoy's 5A Medium, Leibovitz's L-15 Medium, and serum-free media such as EX-CELLTM 300 Series, among others, which can be obtained from the American Type Culture Collection or SAFC Biosciences, as well as other vendors. ..
Modification:Article Title: Mutated PIGGYBAC® transposase
Article Snippet: .. Cell culture media, which may be further supplemented with other components to maximize cell growth, cell viability, and/or recombinant protein production in a particular cultured host cell, are commercially available and include RPMI-1640 Medium, RPMI-1641 Medium, Dulbecco's Modified Eagle's Medium (DMEM), Minimum Essential Medium Eagle, F-12K Medium, Ham's F12 Medium, Iscove's Modified Dulbecco's Medium, McCoy's 5A Medium, Leibovitz's L-15 Medium, and serum-free media such as EX-CELLTM 300 Series, among others, which can be obtained from the American Type Culture Collection or SAFC Biosciences, as well as other vendors. ..
Microscopy:Article Title: Engineering vascularized 3D tissues: An optimized seeding protocol for collagen-based scaffolds
Article Snippet: .. Reagents/tools , Cell line and medium • Primary human umbilical vein endothelial cells, HUVECs (ATCC, Manasses, VA, cat # PCS–100–010) • Vascular cell basal medium (ATCC, cat # PCS–100–030) supplemented with endothelial cell growth kit-VEGF (ATCC, No. PCS–100–041) and 1 % penicillin/streptomycin (ThermoFisher, cat # 15,140,122) Equipment • PHCbi CO 2 Incubator • Countess 3 Automated Cell Counter (ThermoFisher Scientific) • NuWind Multi-Application Centrifuge • Leica TCS SP5 confocal microscope Reagents • Dulbecco’s phosphate-buffered saline (DPBS, ThermoFisher Scientific, cat # 14,040,182) • Trypsin-EDTA (ATCC, cat # 30–2101) • Cubic collagen-based Spongostan Dental MS0005 (Ethicon, Johnson & Johnson) • 4 % paraformaldehyde (PFA, Boster, cat # AR1068) • Phosphate buffered saline (PBS, ThermoFisher Scientific, cat # 10,010,023) • 1 % bovine serum albumin (BSA, Biophoretics, cat # BCZ11920.1 ) • Phalloidin (FITC, ThermoFisher Scientific, cat # F432) • 4′,6-diamidino-2-phenylindole (DAPI, Invitrogen, cat # D1306) Software • LAS AF software • ImageJ Angiogenesis Analysis • GraphPad Prism 10.5.0 Plasticware • T75 cm 2 cell culture flasks (VWR, cat # 10,062–860) • 15 ml conical centrifuge tubes (Oxford Lab Products, cat # OCT-15B) • 0.65 mL microcentrifuge tubes (VWR, cat # 87,003–290) • 12-well plates (VWR, cat # 10,861–556) • Scalpel handle #3 • Sterile surgical carbon steel blades (P&P Medical Surgical, size 10) • Tweezers • 20 μL sterile pipette tips (Oxford Lab Products, cat # XR-20-SLF) • 200 μL sterile pipette tips (Oxford Lab Products, cat # XR-200-SLF) • 1000 μL sterile pipette tips (Oxford Lab Products, cat # XR-1000-SLF) • 20 μL pipette (Eppendorf, cat # ES-20F) • 200 μL pipette (Eppendorf, cat # ES-200F) • 1000 μL pipette (Eppendorf, cat # ES-1000F) • 5 mL serological pipettes (Oxford Lab Products, cat # OSC-5C) • 10 mL serological pipettes (Oxford Lab Products, cat # OSP-10C). .. Experimental design , Endothelial cells were seeded in a commercial 3D collagen scaffold to achieve a vascular network. Scaffolded cells were dyed with DAPI and FITC to visualize branching, which was further quantified using ImageJ Angiogenesis Analysis. Scaffold saturation, cell density, one-sided and two-sided seeding, and incubation period were altered to determine the optimal method for achieving maximal vascularization and branching..
Saline:Article Title: Engineering vascularized 3D tissues: An optimized seeding protocol for collagen-based scaffolds
Article Snippet: .. Reagents/tools , Cell line and medium • Primary human umbilical vein endothelial cells, HUVECs (ATCC, Manasses, VA, cat # PCS–100–010) • Vascular cell basal medium (ATCC, cat # PCS–100–030) supplemented with endothelial cell growth kit-VEGF (ATCC, No. PCS–100–041) and 1 % penicillin/streptomycin (ThermoFisher, cat # 15,140,122) Equipment • PHCbi CO 2 Incubator • Countess 3 Automated Cell Counter (ThermoFisher Scientific) • NuWind Multi-Application Centrifuge • Leica TCS SP5 confocal microscope Reagents • Dulbecco’s phosphate-buffered saline (DPBS, ThermoFisher Scientific, cat # 14,040,182) • Trypsin-EDTA (ATCC, cat # 30–2101) • Cubic collagen-based Spongostan Dental MS0005 (Ethicon, Johnson & Johnson) • 4 % paraformaldehyde (PFA, Boster, cat # AR1068) • Phosphate buffered saline (PBS, ThermoFisher Scientific, cat # 10,010,023) • 1 % bovine serum albumin (BSA, Biophoretics, cat # BCZ11920.1 ) • Phalloidin (FITC, ThermoFisher Scientific, cat # F432) • 4′,6-diamidino-2-phenylindole (DAPI, Invitrogen, cat # D1306) Software • LAS AF software • ImageJ Angiogenesis Analysis • GraphPad Prism 10.5.0 Plasticware • T75 cm 2 cell culture flasks (VWR, cat # 10,062–860) • 15 ml conical centrifuge tubes (Oxford Lab Products, cat # OCT-15B) • 0.65 mL microcentrifuge tubes (VWR, cat # 87,003–290) • 12-well plates (VWR, cat # 10,861–556) • Scalpel handle #3 • Sterile surgical carbon steel blades (P&P Medical Surgical, size 10) • Tweezers • 20 μL sterile pipette tips (Oxford Lab Products, cat # XR-20-SLF) • 200 μL sterile pipette tips (Oxford Lab Products, cat # XR-200-SLF) • 1000 μL sterile pipette tips (Oxford Lab Products, cat # XR-1000-SLF) • 20 μL pipette (Eppendorf, cat # ES-20F) • 200 μL pipette (Eppendorf, cat # ES-200F) • 1000 μL pipette (Eppendorf, cat # ES-1000F) • 5 mL serological pipettes (Oxford Lab Products, cat # OSC-5C) • 10 mL serological pipettes (Oxford Lab Products, cat # OSP-10C). .. Experimental design , Endothelial cells were seeded in a commercial 3D collagen scaffold to achieve a vascular network. Scaffolded cells were dyed with DAPI and FITC to visualize branching, which was further quantified using ImageJ Angiogenesis Analysis. Scaffold saturation, cell density, one-sided and two-sided seeding, and incubation period were altered to determine the optimal method for achieving maximal vascularization and branching..
Software:Article Title: Engineering vascularized 3D tissues: An optimized seeding protocol for collagen-based scaffolds
Article Snippet: .. Reagents/tools , Cell line and medium • Primary human umbilical vein endothelial cells, HUVECs (ATCC, Manasses, VA, cat # PCS–100–010) • Vascular cell basal medium (ATCC, cat # PCS–100–030) supplemented with endothelial cell growth kit-VEGF (ATCC, No. PCS–100–041) and 1 % penicillin/streptomycin (ThermoFisher, cat # 15,140,122) Equipment • PHCbi CO 2 Incubator • Countess 3 Automated Cell Counter (ThermoFisher Scientific) • NuWind Multi-Application Centrifuge • Leica TCS SP5 confocal microscope Reagents • Dulbecco’s phosphate-buffered saline (DPBS, ThermoFisher Scientific, cat # 14,040,182) • Trypsin-EDTA (ATCC, cat # 30–2101) • Cubic collagen-based Spongostan Dental MS0005 (Ethicon, Johnson & Johnson) • 4 % paraformaldehyde (PFA, Boster, cat # AR1068) • Phosphate buffered saline (PBS, ThermoFisher Scientific, cat # 10,010,023) • 1 % bovine serum albumin (BSA, Biophoretics, cat # BCZ11920.1 ) • Phalloidin (FITC, ThermoFisher Scientific, cat # F432) • 4′,6-diamidino-2-phenylindole (DAPI, Invitrogen, cat # D1306) Software • LAS AF software • ImageJ Angiogenesis Analysis • GraphPad Prism 10.5.0 Plasticware • T75 cm 2 cell culture flasks (VWR, cat # 10,062–860) • 15 ml conical centrifuge tubes (Oxford Lab Products, cat # OCT-15B) • 0.65 mL microcentrifuge tubes (VWR, cat # 87,003–290) • 12-well plates (VWR, cat # 10,861–556) • Scalpel handle #3 • Sterile surgical carbon steel blades (P&P Medical Surgical, size 10) • Tweezers • 20 μL sterile pipette tips (Oxford Lab Products, cat # XR-20-SLF) • 200 μL sterile pipette tips (Oxford Lab Products, cat # XR-200-SLF) • 1000 μL sterile pipette tips (Oxford Lab Products, cat # XR-1000-SLF) • 20 μL pipette (Eppendorf, cat # ES-20F) • 200 μL pipette (Eppendorf, cat # ES-200F) • 1000 μL pipette (Eppendorf, cat # ES-1000F) • 5 mL serological pipettes (Oxford Lab Products, cat # OSC-5C) • 10 mL serological pipettes (Oxford Lab Products, cat # OSP-10C). .. Experimental design , Endothelial cells were seeded in a commercial 3D collagen scaffold to achieve a vascular network. Scaffolded cells were dyed with DAPI and FITC to visualize branching, which was further quantified using ImageJ Angiogenesis Analysis. Scaffold saturation, cell density, one-sided and two-sided seeding, and incubation period were altered to determine the optimal method for achieving maximal vascularization and branching..
Sterility:Article Title: Engineering vascularized 3D tissues: An optimized seeding protocol for collagen-based scaffolds
Article Snippet: .. Reagents/tools , Cell line and medium • Primary human umbilical vein endothelial cells, HUVECs (ATCC, Manasses, VA, cat # PCS–100–010) • Vascular cell basal medium (ATCC, cat # PCS–100–030) supplemented with endothelial cell growth kit-VEGF (ATCC, No. PCS–100–041) and 1 % penicillin/streptomycin (ThermoFisher, cat # 15,140,122) Equipment • PHCbi CO 2 Incubator • Countess 3 Automated Cell Counter (ThermoFisher Scientific) • NuWind Multi-Application Centrifuge • Leica TCS SP5 confocal microscope Reagents • Dulbecco’s phosphate-buffered saline (DPBS, ThermoFisher Scientific, cat # 14,040,182) • Trypsin-EDTA (ATCC, cat # 30–2101) • Cubic collagen-based Spongostan Dental MS0005 (Ethicon, Johnson & Johnson) • 4 % paraformaldehyde (PFA, Boster, cat # AR1068) • Phosphate buffered saline (PBS, ThermoFisher Scientific, cat # 10,010,023) • 1 % bovine serum albumin (BSA, Biophoretics, cat # BCZ11920.1 ) • Phalloidin (FITC, ThermoFisher Scientific, cat # F432) • 4′,6-diamidino-2-phenylindole (DAPI, Invitrogen, cat # D1306) Software • LAS AF software • ImageJ Angiogenesis Analysis • GraphPad Prism 10.5.0 Plasticware • T75 cm 2 cell culture flasks (VWR, cat # 10,062–860) • 15 ml conical centrifuge tubes (Oxford Lab Products, cat # OCT-15B) • 0.65 mL microcentrifuge tubes (VWR, cat # 87,003–290) • 12-well plates (VWR, cat # 10,861–556) • Scalpel handle #3 • Sterile surgical carbon steel blades (P&P Medical Surgical, size 10) • Tweezers • 20 μL sterile pipette tips (Oxford Lab Products, cat # XR-20-SLF) • 200 μL sterile pipette tips (Oxford Lab Products, cat # XR-200-SLF) • 1000 μL sterile pipette tips (Oxford Lab Products, cat # XR-1000-SLF) • 20 μL pipette (Eppendorf, cat # ES-20F) • 200 μL pipette (Eppendorf, cat # ES-200F) • 1000 μL pipette (Eppendorf, cat # ES-1000F) • 5 mL serological pipettes (Oxford Lab Products, cat # OSC-5C) • 10 mL serological pipettes (Oxford Lab Products, cat # OSP-10C). .. Experimental design , Endothelial cells were seeded in a commercial 3D collagen scaffold to achieve a vascular network. Scaffolded cells were dyed with DAPI and FITC to visualize branching, which was further quantified using ImageJ Angiogenesis Analysis. Scaffold saturation, cell density, one-sided and two-sided seeding, and incubation period were altered to determine the optimal method for achieving maximal vascularization and branching..
Transferring:Article Title: Engineering vascularized 3D tissues: An optimized seeding protocol for collagen-based scaffolds
Article Snippet: .. Reagents/tools , Cell line and medium • Primary human umbilical vein endothelial cells, HUVECs (ATCC, Manasses, VA, cat # PCS–100–010) • Vascular cell basal medium (ATCC, cat # PCS–100–030) supplemented with endothelial cell growth kit-VEGF (ATCC, No. PCS–100–041) and 1 % penicillin/streptomycin (ThermoFisher, cat # 15,140,122) Equipment • PHCbi CO 2 Incubator • Countess 3 Automated Cell Counter (ThermoFisher Scientific) • NuWind Multi-Application Centrifuge • Leica TCS SP5 confocal microscope Reagents • Dulbecco’s phosphate-buffered saline (DPBS, ThermoFisher Scientific, cat # 14,040,182) • Trypsin-EDTA (ATCC, cat # 30–2101) • Cubic collagen-based Spongostan Dental MS0005 (Ethicon, Johnson & Johnson) • 4 % paraformaldehyde (PFA, Boster, cat # AR1068) • Phosphate buffered saline (PBS, ThermoFisher Scientific, cat # 10,010,023) • 1 % bovine serum albumin (BSA, Biophoretics, cat # BCZ11920.1 ) • Phalloidin (FITC, ThermoFisher Scientific, cat # F432) • 4′,6-diamidino-2-phenylindole (DAPI, Invitrogen, cat # D1306) Software • LAS AF software • ImageJ Angiogenesis Analysis • GraphPad Prism 10.5.0 Plasticware • T75 cm 2 cell culture flasks (VWR, cat # 10,062–860) • 15 ml conical centrifuge tubes (Oxford Lab Products, cat # OCT-15B) • 0.65 mL microcentrifuge tubes (VWR, cat # 87,003–290) • 12-well plates (VWR, cat # 10,861–556) • Scalpel handle #3 • Sterile surgical carbon steel blades (P&P Medical Surgical, size 10) • Tweezers • 20 μL sterile pipette tips (Oxford Lab Products, cat # XR-20-SLF) • 200 μL sterile pipette tips (Oxford Lab Products, cat # XR-200-SLF) • 1000 μL sterile pipette tips (Oxford Lab Products, cat # XR-1000-SLF) • 20 μL pipette (Eppendorf, cat # ES-20F) • 200 μL pipette (Eppendorf, cat # ES-200F) • 1000 μL pipette (Eppendorf, cat # ES-1000F) • 5 mL serological pipettes (Oxford Lab Products, cat # OSC-5C) • 10 mL serological pipettes (Oxford Lab Products, cat # OSP-10C). .. Experimental design , Endothelial cells were seeded in a commercial 3D collagen scaffold to achieve a vascular network. Scaffolded cells were dyed with DAPI and FITC to visualize branching, which was further quantified using ImageJ Angiogenesis Analysis. Scaffold saturation, cell density, one-sided and two-sided seeding, and incubation period were altered to determine the optimal method for achieving maximal vascularization and branching..
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