Proteomic landscape of the primary somatosensory cortex upon sensory deprivation
We employed label free quantitative mass spectrometry to address experience-dependent changes in the proteome after sensory deprivation in 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.
Sample Processing Protocol
Pups were bilaterally spared or deprived off of their C-row whiskers between P12 and P23-P26. The whisker deprivation was repeated every third day to ensure that there was no regrowth of the whiskers. 400 µm thalamocortical slices were prepared. L4 and L2/3 were isolated from barrel cortical columns A-E under a microscope using a pulled patch pipette; tissue from columns A and B were pooled with tissue from columns E and D, respectively. Proteins were isolated in a SDS buffer, denatured with high urea and purified on a 30 kDa filter according to the so called FASP protocol. Digestion was done with trypsin and tryptic peptides were desalted on C18 StageTips. Peptides were seperated with an 25 cm C18 HPLC column and sequenced on a Orbitrap Tribrid Fusion mass spectrometer.
Data Processing Protocol
Raw data was analysed using MaxQuant version 220.127.116.11. with match-between-runs, label-free quantification and intensity based absolute quantification (iBAQ) enabled. The RefSeq protein sequence database downloaded at 28-06-2016 was used to identify proteins.
Corresponding dataset(s) in other omics resources
GSE90929 (GEO, NCBI)
Kole K, Lindeboom RGH, Baltissen MPA, Jansen PWTC, Vermeulen M, Tiesinga P, Celikel T. Proteomic landscape of the primary somatosensory cortex upon sensory deprivation. Gigascience. 2017 6(10):1-10 PubMed: 29020746