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Data released on August 16, 2017

Supporting data for "Proteomic landscape of the primary somatosensory cortex upon sensory deprivation"

Kole, K; Baltissen, M; Lindeboom, R; Jansen, P; Vermeulen, M; Tiesinga, P; Celikel, T (2017): Supporting data for "Proteomic landscape of the primary somatosensory cortex upon sensory deprivation" GigaScience Database. http://dx.doi.org/10.5524/100336 RIS BibTeX Text

Experience-dependent plasticity (EDP) powerfully shapes neural circuits by inducing long-lasting molecular changes in the brain. Molecular mechanisms of EDP have been traditionally studied by identifying single or small subsets of targets along the biochemical pathways that link synaptic receptors to nuclear processes. Recent technological advances in large-scale analysis of gene transcription and translation now allow systematic observation of thousands of molecules simultaneously. Here we employed label-free quantitative mass spectrometry to address experience-dependent changes in the proteome after sensory deprivation of the primary somatosensory cortex.
Cortical column- and layer-specific tissue samples were collected from control animals, with all whiskers intact, and animals whose C-row whiskers were bilaterally plucked for 11-14 days. 33 samples from cortical layers (L) 2/3 and L4 spanning across control, deprived, 1st and 2nd order spared columns yielded at least 10,000 peptides mapping to ~5000 protein groups. Of these, 4,676 were identified with high confidence and >3000 are found in all samples. This comprehensive database provides a snapshot of the proteome after whisker deprivation, a protocol that has been widely used to unravel the synaptic, cellular and network mechanisms of EDP. Complementing the recently made available transcriptome for identical experimental conditions (see DOI:10.5524/100296), the database can be used to (1) mine novel targets whose translation is modulated by sensory organ use, (2) cross-validate experimental protocols from the same developmental time point, and (3) statistically map the molecular pathways of cortical plasticity at a columnar and laminar resolution.

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Related datasets:

doi:10.5524/100336 Cites doi:10.5524/100296

Accessions (data included in GigaDB):

PX: PXD005971

Keywords:

Barrel cortex, whisker plucking, juvenile mice, mass-spectrometry, label-free quantification, proteomics 

Proteomic

http://gigadb.org/images/data/cropped/100336.jpg

Funding:

  • Funding body - Radboud University Nijmegen Faculty of Science
  • Award ID - 626830 – 6200821
  • Awardee - Mr. Paul Tiesinga
  • Funding body - NWO – ALW Open Programme
  • Award ID - 824.14.022
  • Awardee - Mr. Tansu Celikel

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Mouse 2010090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:Protein
Geographic location (latitude and longitude):51.82...
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Mouse 2110090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:Protein
Geographic location (latitude and longitude):51.82...
...
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Mouse 2410090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:Protein
Geographic location (latitude and longitude):51.82...
...
+
Mouse 3610090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:Protein
Geographic location (latitude and longitude):51.82...
...
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Mouse 3710090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:Protein
Geographic location (latitude and longitude):51.82...
...
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Mouse 3810090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:Protein
Geographic location (latitude and longitude):51.82...
...
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Mouse 3910090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:Protein
Geographic location (latitude and longitude):51.82...
...
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Displaying 1-7 of 7 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 
Tabular DataUNKNOWN1.26 MB2017-07-30
ReadmeTEXT2.86 KB2017-07-30
Tabular DataUNKNOWN70.4 KB2017-07-30
Tabular DataUNKNOWN328.72 KB2017-07-30
Tabular DataEXCEL19.32 MB2017-07-30
TextTEXT-0 KB2017-07-30
Displaying 1-6 of 6 File(s).

History:

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