cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25444/nhlbi.14204330
title: HeLa (Cilengitide treatment or MBCD treatment) PREM membrane images supporting "The structure and spontaneous curvature of clathrin lattices at the plasma membrane"

description: This dataset is part of a collection of platinum replica electron microscopy data ( https://doi.org/10.25444/nhlbi.c.5334212) from the manuscript entitled:<br>"The structure and spontaneous curvature of clathrin lattices at the plasma membrane" by Sochacki et al. 2021 (https://doi.org/10.1016/j.devcel.2021.03.017).<br><br>Figure 4 of this manuscript performs several drug treatments on HeLa cells to understand their impact on clathrin structure. Treatments include DMSO, actin inhibiting drugs (https://doi.org/10.25444/nhlbi.14204363; Latrunculin A, Jasplikinolide, Cytochalasin D), cholesterol removal (MBCD), and selective integrin blocking (cilengitide).<br><br>All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). <br><br>HeLa cells were treated with drugs to remove cholesterol (methyl-β-cyclodextrin) or block the binding of aVB5 integrin (Cilengitide). Removing cholesterol caused an increase in flat clathrin while blocking integrins caused a decrease in flat clathrin. Additionally, MBCD treated cells were incubated 5 minutes after unroofing in minimal media to find if the flat clathrin could spontaneously curve. All of these data can be compared to untreated HeLa cells uploaded into a different dataset.HeLa (ATCC® CCL-2™, female human cervix epithelial, adenocarcinoma) cells were grown in DMEM media supplemented with 10% fetal bovine serum , Glutamax, and sodium pyruvate. They were grown on Poly-lysine coated coverslips for one day prior to unroofing. They were treated with Cilengitide (10 µM, Sigma-Aldrich, SML1594) or methyl-β-cyclodextrin (9.5 µM, Sigma-Aldrich C4555) added to growth media at normal growth conditions for one hour prior to unroofing/fixation.They were rinsed briefly with unroofing buffer (30mM HEPES, 70mM KCl, 5mM MgCl2, 3mM EGTA at pH 7.4) prior to unroofing. They were unroofed by brief sonication pulse in the presence of 0.5% paraformaldehyde or direct syringe flow in the presence of 2% paraformaldehyde. The coverslips were then moved immediately into unroofing buffer containing 2% glutaraldehyde. For the methyl-β-cyclodextrin (MBCD) 5 minute data, the membranes were unroofed with no fixative present. They were then incubated in stabilization buffer containing MBCD for 5 minutes before being fixed with glutaraldehyde. <br>Cells were kept in glutaraldehyde at 4 degs C until ready for staining and dehydration; less than two days. The cells were stained with 0.1% tannic acid for 20 minutes, rinsed, then stained with 0.1% uranyl acetate for 20 minutes and dehydrated slowly through a series of increasing ethanol concentration to 100% ethanol. The coverslips were then dried with critical point drying and rotary shadowed with platinum and carbon. The replicas were released from the coverslip with hydrofluoric acid and placed onto a TEM grid for imaging. TEM imaging of replicas was performed on a JEOL 1400 equipped with SerialEM freeware for montaging.
DOI: 10.25444/nhlbi.14204363
title: HeLa (DMSO or actin drug treated) PREM membrane images supporting "The structure and spontaneous curvature of clathrin lattices at the plasma membrane"

description: This dataset is part of a collection of platinum replica electron microscopy data (https://doi.org/10.25444/nhlbi.c.5334212) from the manuscript entitled: "The structure and spontaneous curvature of clathrin lattices at the plasma membrane. " by Sochacki et al. 2021 (https://doi.org/10.1016/j.devcel.2021.03.017). <br>Figure 4 of this manuscript performs several drug treatments on HeLa cells to understand their impact on clathrin structure. Treatments include DMSO, actin inhibiting drugs (Latrunculin A, Jasplikinolide, Cytochalasin D), cholesterol removal (MBCD), and selective integrin blocking (cilengitide) (MBCD and cilengitide at https://doi.org/10.25444/nhlbi.14204330). <br>All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). <br><br>HeLa cells were treated with actin blocking drugs (Jasplakinolide, Latrunculin A, and Cytochalasin D) or a DMSO control. All of these data can be compared to untreated HeLa cells uploaded into a different dataset.HeLa (ATCC® CCL-2™, female human cervix epithelial, adenocarcinoma) cells were grown in DMEM media supplemented with 10% fetal bovine serum , Glutamax, and sodium pyruvate. They were grown on Poly-lysine coated coverslips for one day prior to unroofing. They were treated Jasplakinolide (Millipore 420127), Latrunculin A (Millipore 428021), or Cytochalasin D (Millipore 504776) used at 1:1000 dilution from DMSO stock with a final concentration of 1 µM, 1µM or 10 µM respectively for 15 minutes prior to unroofing/fixation.They were rinsed briefly with unroofing buffer (30mM HEPES, 70mM KCl, 5mM MgCl2, 3mM EGTA at pH 7.4) prior to unroofing. They were unroofed by brief sonication pulse in the presence of 0.5% paraformaldehyde or direct syringe flow in the presence of 2% paraformaldehyde. The coverslips were then moved immediately into unroofing buffer containing 2% glutaraldehyde. For the methyl-β-cyclodextrin (MBCD) 5 minute data, the membranes were unroofed with no fixative present. They were then incubated in stabilization buffer containing MBCD for 5 minutes before being fixed with glutaraldehyde. <br>Cells were kept in glutaraldehyde at 4 degs C until ready for staining and dehydration; less than two days. The cells were stained with 0.1% tannic acid for 20 minutes, rinsed, then stained with 0.1% uranyl acetate for 20 minutes and dehydrated slowly through a series of increasing ethanol concentration to 100% ethanol. The coverslips were then dried with critical point drying and rotary shadowed with platinum and carbon. The replicas were released from the coverslip with hydrofluoric acid and placed onto a TEM grid for imaging. TEM imaging of replicas was performed on a JEOL 1400 equipped with SerialEM freeware for montaging.
DOI: 10.25444/nhlbi.14204363.v1
title: HeLa (DMSO or actin drug treated) PREM membrane images supporting "The structure and spontaneous curvature of clathrin lattices at the plasma membrane"

description: This dataset is part of a collection of platinum replica electron microscopy data (https://doi.org/10.25444/nhlbi.c.5334212) from the manuscript entitled: "The structure and spontaneous curvature of clathrin lattices at the plasma membrane. " by Sochacki et al. 2021 (https://doi.org/10.1016/j.devcel.2021.03.017). <br>Figure 4 of this manuscript performs several drug treatments on HeLa cells to understand their impact on clathrin structure. Treatments include DMSO, actin inhibiting drugs (Latrunculin A, Jasplikinolide, Cytochalasin D), cholesterol removal (MBCD), and selective integrin blocking (cilengitide) (MBCD and cilengitide at https://doi.org/10.25444/nhlbi.14204330). <br>All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). <br><br>HeLa cells were treated with actin blocking drugs (Jasplakinolide, Latrunculin A, and Cytochalasin D) or a DMSO control. All of these data can be compared to untreated HeLa cells uploaded into a different dataset.HeLa (ATCC® CCL-2™, female human cervix epithelial, adenocarcinoma) cells were grown in DMEM media supplemented with 10% fetal bovine serum , Glutamax, and sodium pyruvate. They were grown on Poly-lysine coated coverslips for one day prior to unroofing. They were treated Jasplakinolide (Millipore 420127), Latrunculin A (Millipore 428021), or Cytochalasin D (Millipore 504776) used at 1:1000 dilution from DMSO stock with a final concentration of 1 µM, 1µM or 10 µM respectively for 15 minutes prior to unroofing/fixation.They were rinsed briefly with unroofing buffer (30mM HEPES, 70mM KCl, 5mM MgCl2, 3mM EGTA at pH 7.4) prior to unroofing. They were unroofed by brief sonication pulse in the presence of 0.5% paraformaldehyde or direct syringe flow in the presence of 2% paraformaldehyde. The coverslips were then moved immediately into unroofing buffer containing 2% glutaraldehyde. For the methyl-β-cyclodextrin (MBCD) 5 minute data, the membranes were unroofed with no fixative present. They were then incubated in stabilization buffer containing MBCD for 5 minutes before being fixed with glutaraldehyde. <br>Cells were kept in glutaraldehyde at 4 degs C until ready for staining and dehydration; less than two days. The cells were stained with 0.1% tannic acid for 20 minutes, rinsed, then stained with 0.1% uranyl acetate for 20 minutes and dehydrated slowly through a series of increasing ethanol concentration to 100% ethanol. The coverslips were then dried with critical point drying and rotary shadowed with platinum and carbon. The replicas were released from the coverslip with hydrofluoric acid and placed onto a TEM grid for imaging. TEM imaging of replicas was performed on a JEOL 1400 equipped with SerialEM freeware for montaging.
DOI: 10.15156/bio/sh1229763.08fu
title: SH1229763.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1229764.08fu
title: SH1229764.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/th029469
title: TH029469
title: Rafflesiaceae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.15156/bio/th029470
title: TH029470
title: Podostemaceae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.25444/nhlbi.14195129.v1
title: 3T3-L1 cell PREM membrane images supporting "The structure and spontaneous curvature of clathrin lattices at the plasma membrane"

description: This dataset is part of a collection of platinum replica electron microscopy data (https://doi.org/10.25444/nhlbi.c.5334212) from the manuscript entitled: "The structure and spontaneous curvature of clathrin lattices at the plasma membrane" by Sochacki et al. 2021 (https://doi.org/10.1016/j.devcel.2021.03.017). <br> Figure 1-2 of this manuscript compare the structure of clathrin in eight different cell types: PC12-GR5 (https://doi.org/10.25444/nhlbi.14195507; male rat adrenal gland, pheochromocytoma), 3T3-L1 (https://doi.org/10.25444/nhlbi.14195129; ATCC® CL-173™, male mouse embryo fibroblast), BS-C-1 (https://doi.org/10.25444/nhlbi.14195216; ATCC® CCL-26™, Cercopithecus aethiops, kidney epithelial, sex unknown), HeLa (https://doi.org/10.25444/nhlbi.14195480; ATCC® CCL-2™, female human cervix epithelial, adenocarcinoma), L6 (https://doi.org/10.25444/nhlbi.14195489; ATCC® CRL-1458™, male rat skeletal muscle, myoblast), MCF7 (https://doi.org/10.25444/nhlbi.14195504; ATCC® HTB-22™, female human mammary gland, epithelial, adenocarcinoma), RAW264.7 (https://doi.org/10.25444/nhlbi.14195537; ATCC® TIB-71™, male mouse, Abelson murine leukemia virus-induced tumor, monocyte/macrophage), and U-87 MG https://doi.org/10.25444/nhlbi.14195561; ATCC® HTB-14™, male human, brain, epithelial, likely glioblastoma).<br><br>All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). <br><br>3T3-L1 (ATCC CL-173, male mouse embryo fibroblast) cells were grown in DMEM media supplemented with 10% fetal bovine serum , Glutamax, and sodium pyruvate. They were grown on Poly-lysine coated coverslips for one day prior to unroofing. They were rinsed briefly with unroofing buffer (30mM HEPES, 70mM KCl, 5mM MgCl2, 3mM EGTA at pH 7.4) prior to unroofing. They were unroofed by brief sonication pulse in the presence of 0.5% paraformaldehyde or direct syringe flow in the presence of 2% paraformaldehyde. The coverslips were then moved immediately into unroofing buffer containing 2% glutaraldehyde.Cells were kept in glutaraldehyde at 4 degs C until ready for staining and dehydration; less than two days. The cells were stained with 0.1% tannic acid for 20 minutes, rinsed, then stained with 0.1% uranyl acetate for 20 minutes and dehydrated slowly through a series of increasing ethanol concentration to 100% ethanol. The coverslips were then dried with critical point drying and rotary shadowed with platinum and carbon. The replicas were released from the coverslip with hydrofluoric acid and placed onto a TEM grid for imaging. TEM imaging of replicas was performed on a JEOL 1400 equipped with SerialEM freeware for montaging.<br>
DOI: 10.25444/nhlbi.14195216.v1
title: BSC1 cell PREM membrane images supporting "The structure and spontaneous curvature of clathrin lattices at the plasma membrane"

description: This dataset is part of a collection of platinum replica electron microscopy data (https://doi.org/10.25444/nhlbi.c.5334212) from the manuscript entitled: "The structure and spontaneous curvature of clathrin lattices at the plasma membrane" by Sochacki et al. 2021 (https://doi.org/10.1016/j.devcel.2021.03.017).<br><br> Figure 1-2 of this manuscript compare the structure of clathrin in eight different cell types: PC12-GR5 (https://doi.org/10.25444/nhlbi.14195507; male rat adrenal gland, pheochromocytoma), 3T3-L1 (https://doi.org/10.25444/nhlbi.14195129; ATCC® CL-173™, male mouse embryo fibroblast), BS-C-1 (https://doi.org/10.25444/nhlbi.14195216; ATCC® CCL-26™, Cercopithecus aethiops, kidney epithelial, sex unknown), HeLa (https://doi.org/10.25444/nhlbi.14195480; ATCC® CCL-2™, female human cervix epithelial, adenocarcinoma), L6 (https://doi.org/10.25444/nhlbi.14195489; ATCC® CRL-1458™, male rat skeletal muscle, myoblast), MCF7 (https://doi.org/10.25444/nhlbi.14195504; ATCC® HTB-22™, female human mammary gland, epithelial, adenocarcinoma), RAW264.7 (https://doi.org/10.25444/nhlbi.14195537; ATCC® TIB-71™, male mouse, Abelson murine leukemia virus-induced tumor, monocyte/macrophage), and U-87 MG https://doi.org/10.25444/nhlbi.14195561; ATCC® HTB-14™, male human, brain, epithelial, likely glioblastoma).<br><br>All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). <br><br>BS-C-1 (ATCC CCL-26, Cercopithecus aethiops, kidney epithelial, sex unknown) cells were grown in DMEM media supplemented with 10% fetal bovine serum , Glutamax, and sodium pyruvate. They were grown on Poly-lysine coated coverslips for one day prior to unroofing. They were rinsed briefly with unroofing buffer (30mM HEPES, 70mM KCl, 5mM MgCl2, 3mM EGTA at pH 7.4) prior to unroofing. They were unroofed by brief sonication pulse in the presence of 0.5% paraformaldehyde or direct syringe flow in the presence of 2% paraformaldehyde. The coverslips were then moved immediately into unroofing buffer containing 2% glutaraldehyde.Cells were kept in glutaraldehyde at 4 degs C until ready for staining and dehydration; less than two days. The cells were stained with 0.1% tannic acid for 20 minutes, rinsed, then stained with 0.1% uranyl acetate for 20 minutes and dehydrated slowly through a series of increasing ethanol concentration to 100% ethanol. The coverslips were then dried with critical point drying and rotary shadowed with platinum and carbon. The replicas were released from the coverslip with hydrofluoric acid and placed onto a TEM grid for imaging. TEM imaging of replicas was performed on a JEOL 1400 equipped with SerialEM freeware for montaging.
DOI: 10.25444/nhlbi.14195489
title: L6 cell PREM membrane images supporting "The structure and spontaneous curvature of clathrin lattices at the plasma membrane"

description: This dataset is part of a collection of platinum replica electron microscopy data (https://doi.org/10.25444/nhlbi.c.5334212) from the manuscript entitled: "The structure and spontaneous curvature of clathrin lattices at the plasma membrane" by Sochacki et al. 2021 (https://doi.org/10.1016/j.devcel.2021.03.017). <br> Figure 1-2 of this manuscript compare the structure of clathrin in eight different cell types: PC12-GR5 (https://doi.org/10.25444/nhlbi.14195507; male rat adrenal gland, pheochromocytoma), 3T3-L1 (https://doi.org/10.25444/nhlbi.14195129; ATCC® CL-173™, male mouse embryo fibroblast), BS-C-1 (https://doi.org/10.25444/nhlbi.14195216; ATCC® CCL-26™, Cercopithecus aethiops, kidney epithelial, sex unknown), HeLa (https://doi.org/10.25444/nhlbi.14195480; ATCC® CCL-2™, female human cervix epithelial, adenocarcinoma), L6 (https://doi.org/10.25444/nhlbi.14195489; ATCC® CRL-1458™, male rat skeletal muscle, myoblast), MCF7 (https://doi.org/10.25444/nhlbi.14195504; ATCC® HTB-22™, female human mammary gland, epithelial, adenocarcinoma), RAW264.7 (https://doi.org/10.25444/nhlbi.14195537; ATCC® TIB-71™, male mouse, Abelson murine leukemia virus-induced tumor, monocyte/macrophage), and U-87 MG https://doi.org/10.25444/nhlbi.14195561; ATCC® HTB-14™, male human, brain, epithelial, likely glioblastoma).<br><br>All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). <br><br>L6 (ATCC® CRL-1458™, male rat skeletal muscle, myoblast) cells were grown in DMEM media supplemented with 10% fetal bovine serum , Glutamax, and sodium pyruvate. They were grown on Poly-lysine coated coverslips for one day prior to unroofing. They were rinsed briefly with unroofing buffer (30mM HEPES, 70mM KCl, 5mM MgCl2, 3mM EGTA at pH 7.4) prior to unroofing. They were unroofed by brief sonication pulse in the presence of 0.5% paraformaldehyde or direct syringe flow in the presence of 2% paraformaldehyde. The coverslips were then moved immediately into unroofing buffer containing 2% glutaraldehyde.Cells were kept in glutaraldehyde at 4 degs C until ready for staining and dehydration; less than two days. The cells were stained with 0.1% tannic acid for 20 minutes, rinsed, then stained with 0.1% uranyl acetate for 20 minutes and dehydrated slowly through a series of increasing ethanol concentration to 100% ethanol. The coverslips were then dried with critical point drying and rotary shadowed with platinum and carbon. The replicas were released from the coverslip with hydrofluoric acid and placed onto a TEM grid for imaging. TEM imaging of replicas was performed on a JEOL 1400 equipped with SerialEM freeware for montaging.
DOI: 10.25444/nhlbi.14195504.v1
title: MCF7 cell PREM membrane images supporting "The structure and spontaneous curvature of clathrin lattices at the plasma membrane"

description: This dataset is part of a collection of platinum replica electron microscopy data (https://doi.org/10.25444/nhlbi.c.5334212) from the manuscript entitled: "The structure and spontaneous curvature of clathrin lattices at the plasma membrane" by Sochacki et al. 2021 (https://doi.org/10.1016/j.devcel.2021.03.017). <br> Figure 1-2 of this manuscript compare the structure of clathrin in eight different cell types: PC12-GR5 (https://doi.org/10.25444/nhlbi.14195507; male rat adrenal gland, pheochromocytoma), 3T3-L1 (https://doi.org/10.25444/nhlbi.14195129; ATCC® CL-173™, male mouse embryo fibroblast), BS-C-1 (https://doi.org/10.25444/nhlbi.14195216; ATCC® CCL-26™, Cercopithecus aethiops, kidney epithelial, sex unknown), HeLa (https://doi.org/10.25444/nhlbi.14195480; ATCC® CCL-2™, female human cervix epithelial, adenocarcinoma), L6 (https://doi.org/10.25444/nhlbi.14195489; ATCC® CRL-1458™, male rat skeletal muscle, myoblast), MCF7 (https://doi.org/10.25444/nhlbi.14195504; ATCC® HTB-22™, female human mammary gland, epithelial, adenocarcinoma), RAW264.7 (https://doi.org/10.25444/nhlbi.14195537; ATCC® TIB-71™, male mouse, Abelson murine leukemia virus-induced tumor, monocyte/macrophage), and U-87 MG https://doi.org/10.25444/nhlbi.14195561; ATCC® HTB-14™, male human, brain, epithelial, likely glioblastoma).<br><br>All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). <br><br>MCF7 (ATCC® HTB-22™, female human mammary gland, epithelial, adenocarcinoma) cells were grown in DMEM media supplemented with 10% fetal bovine serum. They were grown on Poly-lysine coated coverslips for one day prior to unroofing. They were rinsed briefly with unroofing buffer (30mM HEPES, 70mM KCl, 5mM MgCl2, 3mM EGTA at pH 7.4) prior to unroofing. They were unroofed by brief sonication pulse in the presence of 0.5% paraformaldehyde or direct syringe flow in the presence of 2% paraformaldehyde. The coverslips were then moved immediately into unroofing buffer containing 2% glutaraldehyde.Cells were kept in glutaraldehyde at 4 degs C until ready for staining and dehydration; less than two days. The cells were stained with 0.1% tannic acid for 20 minutes, rinsed, then stained with 0.1% uranyl acetate for 20 minutes and dehydrated slowly through a series of increasing ethanol concentration to 100% ethanol. The coverslips were then dried with critical point drying and rotary shadowed with platinum and carbon. The replicas were released from the coverslip with hydrofluoric acid and placed onto a TEM grid for imaging. TEM imaging of replicas was performed on a JEOL 1400 equipped with SerialEM freeware for montaging.