|
| Status |
Public on Aug 17, 2017 |
| Title |
Control_L2/3_3 |
| Sample type |
SRA |
| |
|
| Source name |
Barrel Cortex C Column Layer 2/3
|
| Organism |
Mus musculus |
| Characteristics |
group: Control
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 |
A113
|
| 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 |
SAMN06112881 |
| SRA |
SRX2398380 |
