Pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells

This database is associated with the following publication: Pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells. It includes dSTORM single-molecule localization data, digital microscope time-lapse imaging data, cryo-fracture SEM imaging data, and confocal microscopy imaging data.

STORMdata Haas et al 2020 Molecular Lists.7z

These data were acquired using the Nikon N STORM microscope. The single-molecule detection was performed using Nikon NIS elements software. This dataset contains the dSTORM microscopy data presented in Fig. 1 and 2, figs. S3, S5, S8, and S9 and movies 1 to 6.
It can be analyzed with Matlab based program associated with this publication, Grafeo_v2, and freely available for download at GitHub or Zenodo: DOI: 10.5281/zenodo.3581144
or https://zenodo.org/badge/latestdoi/114145546.
Each folder corresponds to independent experimental preparation and it contains subfolders with names corresponding to the condition, antibody, and fluorophore tag used, e.g., WT - wild type, PME, and PMEI mutant plants; 2F4 and LM20 are the primary antibodies used to tag low and highly methylesterified homogalacturonan, respectively. Each STORM data set has two channels corresponding to CF568 and Alexa 647 dye.
E.g. the folder: 2015_05_20_00631 contains a subfolder: WT_2F4-568_LM20-647, corresponding to WT plant condition where demethylated pectins were detected with 2F4 antibody revealed with secondary antibody conjugated to CF568 fluorophore, etc. The files A647-3d_1.txt, and CF568-3d_1.txt contain the list of the localized single molecules and their attributes (described in the column headers) for two imaging channels, Alexa 647 and CF568 separately. Low-resolution images for both channels are also provided, as well as overall cell wall labeling with CalcoFluor fluorophore (405 nm).

CryoSEMData.7z
This dataset contains Cryo-fracture SEM images presented in Figs. 1, 3 and 4, and fig. S6. These data can be analyzed using Matlab based scripts (SEMfilaments) associated with this publication and available for the download at GitHub or Zenodo :
DOI: 10.5281/zenodo.3581097
or: https://zenodo.org/badge/latestdoi/221728265

DigitalMicroscopeTimelapseData.7z

The data were using Keyence VHX-5000 (KEYENCE (UK) LIMITED Milton Keynes, U.K.) digital microscope and are presented in Fig. 3 and fig. S1 and S10. These data can be analyzed using the Matlab based scripts (ShapeSpectraAnalysis) associated with this publication and available for the download at GitHub or Zenodo : DOI: 10.5281/zenodo.3581129
or: https://zenodo.org/badge/latestdoi/197577846

TissueExpansion.7z
The data were acquired using Zeiss LSM 710 laser scanning confocal microscope (Zeiss Oberkochen Germany).
This dataset includes representative confocal microscopy images presented in Fig. 4 and fig. S10 and the .xls file with analyzed data.

If you need any further details, please do not hesitate to contact Kalina Haas: [e-mail]

本数据库与以下出版物相关联：《pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells》。数据库中包含dSTORM单分子定位数据、数字显微镜时间推移成像数据、冷冻断裂扫描电子显微镜成像数据和共聚焦显微镜成像数据。STORM数据由Haas等人于2020年发布，存储于Molecular Lists.7z文件中。这些数据利用尼康N STORM显微镜获取，单分子检测采用尼康NIS elements软件完成。本数据集涵盖了图1和2、图S3、S5、S8和S9，以及电影1至6中展示的dSTORM显微镜数据。数据可通过与该出版物相关联的Matlab程序Grafeo_v2进行分析，该程序可在GitHub或Zenodo上免费下载：DOI：10.5281/zenodo.3581144 或 https://zenodo.org/badge/latestdoi/114145546。每个文件夹对应独立的实验准备，并包含以条件、抗体和荧光标记命名的子文件夹，例如：WT（野生型）、PME和PMEI突变植物；2F4和LM20为用于标记低和高度甲基化的同半乳糖醛酸的初级抗体。每个STORM数据集包含两个通道，分别对应CF568和Alexa 647染料。例如，文件夹2015_05_20_00631包含子文件夹WT_2F4-568_LM20-647，对应于WT植物条件，其中使用2F4抗体检测去甲基化的果胶，并通过与CF568荧光素偶联的二级抗体进行标记。文件A647-3d_1.txt和CF568-3d_1.txt分别包含两个成像通道（Alexa 647和CF568）中定位的单分子及其属性列表（描述在列标题中）。同时提供了两个通道的低分辨率图像，以及使用CalcoFluor荧光素（405 nm）进行整体细胞壁标记的图像。CryoSEMData.7z数据集包含图1、3和4以及图S6中展示的冷冻断裂扫描电子显微镜图像，这些数据可通过与该出版物相关联的基于Matlab的脚本（SEMfilaments）进行分析，该脚本可在GitHub或Zenodo上免费下载：DOI：10.5281/zenodo.3581097 或 https://zenodo.org/badge/latestdoi/221728265。DigitalMicroscopeTimelapseData.7z数据使用Keyence VHX-5000（KEYENCE (UK) LIMITED Milton Keynes, U.K.）数字显微镜获取，并在图3、图S1和S10中展示。这些数据可通过与该出版物相关联的基于Matlab的脚本（ShapeSpectraAnalysis）进行分析，该脚本可在GitHub或Zenodo上免费下载：DOI：10.5281/zenodo.3581129 或 https://zenodo.org/badge/latestdoi/197577846。TissueExpansion.7z数据使用蔡司LSM 710激光扫描共聚焦显微镜（蔡司Oberkochen Germany）获取。本数据集包括图4和图S10中展示的代表性共聚焦显微镜图像以及分析数据所在的.xls文件。如需了解更多细节，请随时联系Kalina Haas：[e-mail]。