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Data released on August 16, 2017

Supporting data for "Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation"

Benes, V; Celikel, T; Kole, K; Komuro, Y; Pistolic, J; Provaznik, J; Tiesinga, P (2017): Supporting data for "Transcriptional mapping of the primary somatosensory cortex upon sensory deprivation" GigaScience Database. http://dx.doi.org/10.5524/100296 RIS BibTeX Text

Experience-dependent plasticity (EDP) is essential for anatomical and functional maturation of sensory circuits during development. Although the principal synaptic and circuit mechanisms of EDP are increasingly well studied experimentally and computationally, its molecular mechanisms remain largely elusive. EDP can be readily studied in the rodent barrel cortex, where each ‘barrel column’ preferentially represents deflections of its own principal whisker. Depriving select whiskers while sparing their neighbours introduces competition between barrel columns, ultimately leading to weakening of intracortical, translaminar (i.e. Cortical Layer (L)4-to-L2/3) feed-forward excitatory projections in the deprived columns. The same synapses are potentiated in the neighbouring spared columns. These experience-dependent alterations of synaptic strength are thought to underlie somatosensory map plasticity. We used RNA sequencing in this model system to uncover cortical-column and -layer specific changes on the transcriptome level that are induced by altered sensory experience.
Column- and layer-specific barrel cortical tissues were collected from juvenile mice with all whiskers intact and mice that received 11-12 days long whisker (C-row) deprivation before high quality RNA was purified and sequenced. The current dataset entails 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.

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Related manuscripts:

doi:10.1093/gigascience/gix081

Related datasets:

doi:10.5524/100296 IsCitedBy doi:10.5524/100336

Accessions (data included in GigaDB):

GEO: GSE90929

Transcriptomic

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Funding:

  • Funding body - Radboud University Nijmegen Faculty of Science
  • Award ID - 626830 – 6200821
  • Funding body - NWO – ALW Open Programme
  • Award ID - 824.14.022

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Mouse 110090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:RNA
Geographic location (latitude and longitude):51.82...
...
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Mouse 210090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:RNA
Geographic location (latitude and longitude):51.82...
...
+
Mouse 310090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:RNA
Geographic location (latitude and longitude):51.82...
...
+
Mouse 410090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:RNA
Geographic location (latitude and longitude):51.82...
...
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Mouse 510090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:RNA
Geographic location (latitude and longitude):51.82...
...
+
Mouse 610090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:RNA
Geographic location (latitude and longitude):51.82...
...
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Mouse 710090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:RNA
Geographic location (latitude and longitude):51.82...
...
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Mouse 810090Mousehouse mouseMus musculus Description:Wild type mouse, strain C57BL/6
Analyte type:RNA
Geographic location (latitude and longitude):51.82...
...
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Displaying 1-8 of 8 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 
directoryUNKNOWN210.97 MB2017-07-30
ReadmeTEXT2.38 KB2017-07-30
Mixed archiveTAR5.33 KB2017-07-30
Expression dataUNKNOWN2.8 MB2017-07-30
Expression dataEXCEL4.78 MB2017-07-30
otherPDF1.49 MB2017-07-30
ScriptTEXT3.6 KB2017-07-30
Displaying 1-7 of 7 File(s).

History:

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