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Data released on January 08, 2018

Supporting data for “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors”

Lukeš, T; Pospíšil, J; Fliegel, K; Lasser, T; Hagen, G, M (2018): Supporting data for “Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors” GigaScience Database. http://dx.doi.org/10.5524/100400 RIS BibTeX Text

Super-resolution single molecule localization microscopy (SMLM) is a method for achieving resolution beyond the classical limit in optical microscopes (approx. 200 nm laterally). Yellow fluorescent protein (YFP) has been used for superresolution single molecule localization microscopy, but less frequently than other fluorescent probes. Working with YFP in SMLM is a challenge because a lower number of photons are emitted per molecule compared to organic dyes which are more commonly used. Publically available experimental data can facilitate development of new data analysis algorithms. Four complete, freely available single molecule super-resolution microscopy datasets on YFP-tagged growth factor receptors expressed in a human cell line are presented including both raw and analyzed data. We report methods for sample preparation, for data acquisition, and for data analysis, as well as examples of the acquired images. We also analyzed the SMLM data sets using a different method: super-resolution optical fluctuation imaging (SOFI). The two modes of analysis offer complementary information about the sample. A fifth single molecule super-resolution microscopy dataset acquired with the dye Alexa 532 is included for comparison purposes. This dataset has potential for extensive reuse. Complete raw data from SMLM experiments has typically not been published. The YFP data exhibits low signal to noise ratios, making data analysis a challenge. These data sets will be useful to investigators developing their own algorithms for SMLM, SOFI, and related methods. The data will also be useful for researchers investigating growth factor receptors such as ErbB3.

Contact Submitter

Read the peer-reviewed publication(s):

Lukeš, T., Pospíšil, J., Fliegel, K., Lasser, T., & Hagen, G. M. (2018). Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors. GigaScience, 7(3). doi:10.1093/gigascience/giy002

Additional information:

http://zitmen.github.io/thunderstorm/

Keywords:

super-resolution microscopy palm storm sofi yfp smlm single molecule growth factor receptor erbb3 thunderstorm 

Imaging

http://gigadb.org/images/data/cropped/100400.jpg

Funding:

  • Funding body - BioFrontiers Institute University of Colorado
  • Awardee - G Hagen
  • Funding body - České Vysoké Učení Technické v Praze
  • Award ID - SGS16/167/OHK3/2T/13
  • Awardee - K Fliegel
  • Funding body - Grantová Agentura České Republiky
  • Awardee - G Hagen
  • Funding body - SCIEX
  • Award ID - 13.183
  • Awardee - T Lukeš

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Alexa_532_data9606HumanhumanHomo sapiens Description:HeLa cells labelled with 5-fluorouridine to label newly synthesised RNA transcripts, and immunocytochemically labelled with anti-fluorouridine antibody and a secondary antibody labelled with Alexa532
RRID:RRID:CVCL_0030
Cell type:HeLa
YFP_data_19606HumanhumanHomo sapiens Description:Epithelial carcinoma A431 cells expressing mCitrine-ErbB3
RRID:RRID:CVCL_0037
Cell type:A-431
YFP_data_29606HumanhumanHomo sapiens Description:Epithelial carcinoma A431 cells expressing mCitrine-ErbB3
RRID:RRID:CVCL_0037
Cell type:A-431
YFP_data_39606HumanhumanHomo sapiens Description:Epithelial carcinoma A431 cells expressing mCitrine-ErbB3
RRID:RRID:CVCL_0037
Cell type:A-431
YFP_data_49606HumanhumanHomo sapiens Description:Epithelial carcinoma A431 cells expressing mCitrine-ErbB3
RRID:RRID:CVCL_0037
Cell type:A-431
Displaying 1-5 of 5 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
GitHub archivearchive3.14 MB2017-12-22
Tabular dataCSV77.5 KB2018-01-08
Tabular dataCSV67.49 KB2018-01-08
Alexa_532_dataImageTAR1.46 GB2017-12-22
YFP_data_2ImageTAR2.7 GB2017-12-22
YFP_data_4ImageTAR1.4 GB2017-12-22
YFP_data_1ImageTAR5.3 GB2017-12-22
YFP_data_3ImageTAR859.94 MB2017-12-22
TXTTEXT2.24 KB2018-01-08
ReadmeTEXT2.72 KB2017-12-22
Displaying 1-10 of 12 File(s).

History:

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