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Data released on November 24, 2015

Supporting data for "Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis".

Angel, C, E; Crampin, E, J; Cursons, J; Dunbar, P; Hurley, D, G; Jacobs, M, D; Print, C, G (2015): Supporting data for "Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis". GigaScience Database. http://dx.doi.org/10.5524/100168 RIS BibTeX Text

Human epidermis from three patients underwent single-target immunofluorescence labelling against: calmodulin, β1 integrin, β4 integrin, keratin-10, keratin-14, 14-3-3σ (stratifin), Raf-1, phospho-Raf-1 (pS338), MEK-1/2, phospho-MEK-1/2 (pS218/pS222), ERK-1/2, phospho-ERK-1/2 (pT183/pY185), JunB, c-Jun, c-Fos and Fra2.
Confocal microscopy was used to collect image data over a tissue volume, at or near the diffraction limited imaging (x-y) resolution, providing a unique data set that examines signalling proteins in the context of a homeostatic human tissue.
We have recently used bulk changes in the abundance of proteins and phospho-proteins (a subset of these data) for a model of in situ ERK-MAPK activity, driven by Ca2+ signalling inputs. There may be scope in extending such analyses to include a greater range of the data within a model of epidermal keratinocyte differentiation. Furthermore, we believe that researchers who study intercellular heterogeneity of signalling components may find these data useful.
Together with our sampled protein abundance data, we provide some preliminary cellular segmentations. On via our GitHub page, we also provide a collection of MATLAB scripts and segmented data files that allow quantitative analysis of these image data. The intermediate processed files are provided in formats that should allow advanced users to develop their own analyses using open source tools such as python.

Contact Submitter

Related manuscripts:

doi:10.1186/s13742-015-0102-5

Additional information:

http://www.github.com/uomsystemsbiology/epidermal_data

Keywords:

MEK-1/2 calmodulin skin interfollicular keratinocytes immunofluorescence confocal microscopy homeostatic tissue cellular heterogeneity 

Imaging

http://gigadb.org/images/data/cropped/100168.jpg

Funding:

  • Funding body - Treasury, New Zealand
  • Award ID - C08X0801
  • Comment - Marc D Jacobs
  • Funding body - Australian Research Council
  • Award ID - CE140100036
  • Comment - Edmund J Crampin
  • Funding body - Tertiary Education Commission
  • Location - NZ
  • Award ID - Top Achiever Doctoral Scholarship
  • Comment - Joseph Cursons

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Pat_19606HumanhumanHomo sapiens Description:Human skin samples were obtained with ...
Tissue type:skin
Cell type:epidermis
...
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Pat_29606HumanhumanHomo sapiens Description:Human skin samples were obtained with ...
Tissue type:skin
Cell type:epidermis
...
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Pat_39606HumanhumanHomo sapiens Description:Human skin samples were obtained with ...
Tissue type:skin
Cell type:epidermis
...
+
Displaying 1-3 of 3 Sample(s).

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDFile TypeFile FormatSizeRelease Date 
DirectoryUNKNOWN99.29 MB2015-11-05
DirectoryUNKNOWN185.09 MB2015-11-05
Pat_1DirectoryUNKNOWN1.04 MB2015-11-05
Pat_3DirectoryUNKNOWN70.35 MB2015-11-05
Pat_3DirectoryUNKNOWN1.06 MB2015-11-05
Pat_1DirectoryUNKNOWN82.76 MB2015-11-05
Pat_2DirectoryUNKNOWN45.6 MB2015-11-05
Pat_2DirectoryUNKNOWN2.08 MB2015-11-05
Pat_3DirectoryUNKNOWN56.9 MB2015-11-05
Pat_3DirectoryUNKNOWN1.04 MB2015-11-05
Displaying 1-10 of 235 File(s).

History:

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