Developmental Cell

Raw and processed data for all figures in Cell cycle heterogeneity can generate robust cell type proportioning (Dev. Cell, Gruenheit et al. 2018). Each Excel spreadsheet contains the data for one figure, different tabs contain data for subfigures. Three additional figures were also added. The word file contains the figure legends also for these additional figures.

Low temperatures affect plant growth, development, productivity, and ecological distribution. Expression of the C-repeat-binding factor (CBF) transcription factors is induced by cold stress, which in turn activates downstream cold-responsive (COR) genes that are required for the acquisition of freezing tolerance. Inducer of CBF expression 1 (ICE1) is a master regulator of CBFs, and ICE1 stability is crucial for its function. However, the regulation of ICE1 is not well understood. Here, we report that mitogen-activated protein kinase 3 (MPK3) and MPK6 interact with and phosphorylate ICE1, which reduces its stability and transcriptional activity. Consistently, the mpk3 and mpk6 single mutants and the mpk3 mpk6 double mutant show enhanced freezing tolerance, whereas MPK3/MPK6 activation attenuates freezing tolerance. Phosphor-inactive mutations of ICE1 complement freezing sensitivity in the ice1-2 mutant. These combined results indicate that MPK3/MPK6 phosphorylate and destabilize ICE1, which negatively regulates CBF expression and freezing tolerance in plants.

This example dataset is associated with the article "Quantitative multiscale cell imaging in controlled 3D microenvironments" by the same authors published in Developmental Cell in February 2016. These data are used by three Matlab functions (exampleCollagen3D.m, exampleBleb3D.m, exampleSurfaceIntensity3D.m) in the publication's "meSPIM Supplemental Information" zip file to present the computational workflow described in the article. Please see the publication for more information about this dataset.

Research data supporting the publication "A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control". The dataset contains timeseries of the development of 5 WT flowers and 3 timeseries of the development of lfy mutants.

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). 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). All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). 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. 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.

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). 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). Figure 3 of this manuscript shows what happens to clathrin when HeLa cells are unroofed (the top of the cell and the cytoplasm is removed) and the remaining cell membrane is incubated in a minimal medium lacking energy or protein for up to 20 minutes (0,2,5,10,20 min time points). Flat clathrin curves into almost spherical buds over this time period. All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). The idea behind these experiments was to unroof cells and visualize the clathrin on their membranes either in their natural state (0 min, HeLa_membranes_1-4) or after they have been allowed to sit in a minimal media lacking any protein or energy source (HeLa_Xmin_postunroofing). From these experiments, we saw that flat clathrin can curve without added subunits or energy. HeLa (ATCC® CCL-2™, female human cervix epithelial, adenocarcinoma, female) 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.For spontaneous curvature: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 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 pulsebor direct syringe flow with no fixative present. The coverslips were then moved immediately into fresh unroofing buffer for the given amount of time. After either 2,5,10,20 min uncubation period, the cells were placed in 2% glutaraldehyde in unroofing buffer. 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.

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). 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). All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). U-87 MG (ATCC® HTB-14™, male human, brain, epithelial, likely glioblastoma) 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.

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). 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). All images are tiled montages acquired on an AMT XR111 ccd at 15000 x magnification (pixel size 1.2 nm). 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. 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.