| Metadata |
| datasetIdentifier | PASS00080 |
| datasetType | MSMS |
| submitter | Joern Dengjel <joern.dengjel@frias.uni-freiburg.de> |
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| lab_head_full_name | |
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| datasetTag | RDEB_ECM_files |
| datasetTitle | Epidermolysis bullosa disease proteomics: SILAC labeled ECM and CM |
| publicReleaseDate | 2013-03-27 00:00:00 |
| finalizedDate | 2013-03-27 14:25:43 |
| summary | Two datasets were generated: SILAC-labeled extracellular matrix (ECM) and conditioned medium (CM) of primary human skin fibroblasts. Details can be found in the uploaded ReadMe.txt file. |
| contributors | Victoria Küttner, Claudia Mack, Kristoffer T.G. Rigbolt, Johannes S. Kern, Oliver Schilling, Hauke Busch, Leena Bruckner-Tuderman, and Joern Dengjel
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| publication | Küttner et al, Global remodelling of cellular microenvironment due to loss of collagen VII, Mol Sys Biol (2013) |
| growth | Primary skin fibroblasts were kept in culture for 6 days. At day 2, 3, and 4, fresh culture medium containing ascorbate was added. The CM was harvested at day 4 and the ECM at day 6. |
| treatment | Prior CM harvest cells were kept for 14 h without FCS. |
| extraction | The cells were removed from the underlying ECM with 0.5% Triton X-100 in 20 mM NH4OH for 30 seconds. The remaining ECM was then carefully washed 5 x with PBS to eliminate intracellular contaminants. The ECM was solubilised with 4% SDS in 0.1M Tris-HCl, pH 7.6. |
| separation | Mixed, labeled samples were separated by SDS-PAGE. |
| digestion | Proteins were in-gel digested using trypsin (sequencing grade). |
| acquisition | TOP5 data-dependent acquisition on an LTQ-Orbitrap XL. |
| informatics | Data was analyzed by MaxQuant/Andromeda. |
| instruments | Thermo Scientific LTQ Orbitrap XL |
| species | Human |
| massModifications | static: C+57.021464, variable: K+8.014199, R+10.008269, K+4.025107, R+6.020129 |
