Experience-dependent plasticity (EDP) is essential for anatomical and functional maturation of sensory circuits during development, however its molecular mechanisms remain largely elusive. EDP can be readily studied in the rodent barrel cortex, which processes tactile information on whisker (or the mystacial vibrissae). We have previously shown that depriving select whiskers while sparing their neighbours introduces competition between barrel columns, ultimately leading to weakening of intracortical feed-forward excitatory projections in the deprived columns (Allen et al, 2003 and Celikel et al, 2004), the same synapses in the neighbouring spared columns are potentiated (Clem et al, 2008) These experience-dependent, and cortical column- and layer-specific, alterations of synaptic strength are thought to underlie somatosensory map plasticity. To systematically address the molecular mechanisms of EDP we used RNA-sequencing and label-free quantitative mass spectrometry on tissues extracted from juvenile (P23-26) sensory deprived mouse barrel cortex in a column- and layer-specific manner. Samples were collected from cortical layers (L) 2/3 and L4 spanning across control, deprived, 1st and 2nd order spared columns. High quality RNA was purified and sequenced, yielding in a transcriptome-wide dataset entailing an average of 50 million paired-end reads per sample, 75 base pairs in length. On average, 90.15% of reads could be uniquely mapped to the mm10 reference mouse genome. Protein mass spectrometry yielded >10,000 peptides mapping to ~5000 protein groups/sample. Of these, 4,676 were identified with high confidence and >3000 are found across all samples. These datasets are the first correlated transcriptome and proteome that allow mining the molecular correlates of experience-dependent plasticity.

Overview of the experimental design and sample collection.
(A) Experimentally naive pups with all whiskers intact (Control group) and pups that received bilateral C-row deprivation for a period of 12-14 days (Experimental group) were used for these studies. Experimental animals received whisker deprivation every 2-3 days to ensure that whisker regrowth did not interfere with the sensory deprivation. Control animals received sham whisker deprivation. Cortical column and laminae specific tissue were isolated in acute thalamocortical slices on P23-26. (B) Before RNA-sequencing, RNA was isolated and its integrity and purity was checked. For protein mass spectrometry, proteins were denatured and purified, followed by on-filter digestion into tryptic peptides, which were subsequently desalted and sequenced on a mass spectrometer.

Overview of the experimental design and sample collection.

Please refer to the publications below for further details:

Transcriptome: Kole et al (2017). Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation. Gigascience. 6(10) 1-6
Proteome: Kole et al (2017). Proteomic landscape of the primary somatosensory cortex upon sensory deprivation. Gigascience. 6(10) 1-10
Sample preparation: Kole and Celikel (preprint). Neocortical microdissection at columnar and laminar resolution for molecular interrogation. bioRxiv.

Raw and Processed Transcriptomic Data
The raw RNA sequence reads are available at GEO with the accession number GSE90929
BAM File alignments, STAR outputs, gene counts, and EdgeR routines are available via GIGADB, data ID 100296

Raw and Processed Proteomic Data
The raw mass spectrometry data are available via ProteomeXchange Consortium, dataset identifier PXD005971
Copy numbers, peptide counts, and R command lines are available via GIGADB, data ID 100336