|
Status |
Public on Aug 17, 2017 |
Title |
Deprived_L4_4 |
Sample type |
SRA |
|
|
Source name |
Barrel Cortex C Column Layer 4
|
Organism |
Mus musculus |
Characteristics |
group: Deprived age: Postnatal day 23-24 strain: C57BL/6
|
Extracted molecule |
total RNA |
Extraction protocol |
Tissue samples originating from the same animal, columns and layer were pooled. Tissue was quickly dissolved in Qiazol (Qiagen #79306) and RNA was isolated using the miRNeasy Mini kit (Qiagen #217004). The extracted RNA was DNAse treated (Thermo Scientific, #EN0521) and finally cleaned up using RNeasy MinElute kit (Qiagen #74204). The cDNA library was generated using the non-stranded NEBNext Ultra RNA Library Preparation Kit for Illumina (New England Biolabs, catalogue #E7530). For the library enrichment, 13-14 PCR cycles were performed
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
B214
|
Data processing |
Basecalls were performed using Illumina RTA version 2.4.6. Reads were trimmed to 75 bp using Trimmomatic version 0.36, with the configurations: PE (Paired End) and CROP:75 Reads were mapped to the mm10 genome using STAR version 2.5.2a; output for all samples can be found in Genecounts_Colourcoded.xlsx Genome_build: mm10 Supplementary_files_format_and_content: Genecounts_Colourcoded.xlsx contains read counts for all samples after STAR mapping; colours indicate experimental groups (n=4 for all)
|
|
|
Submission date |
Dec 06, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Koen Kole |
E-mail(s) |
k.kole@neurophysiology.nl
|
Organization name |
Donders Institute for Brain Cognition and Behaviour
|
Department |
Neurophysiology
|
Street address |
Heyendaalsweg 135
|
City |
Nijmegen |
ZIP/Postal code |
6525 EN |
Country |
Netherlands |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE90929 |
Transcriptional changes in the primary somatosensory cortex upon sensory deprivation |
|
Relations |
BioSample |
SAMN06112899 |
SRA |
SRX2398401 |