|
| Status |
Public on Aug 27, 2020 |
| Title |
NSD5 |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
Sex: Male
group: Non Sleep deprived
strain: CaMKII-Cre:Ribotag
age: 2-3 months
|
| Treatment protocol |
Animals were gently handled through tapping of the cages and cage shakes for 3 min for three days prior to the scheduled experiment. All sleep deprivation was performed starting at the beginning of the light-dark cycle to avoid circadian confounds. Sleep deprivation was performed using gentle handling through cage tapping and then cage shakes as necessary. To ensure that only the minimal amount of disturbance was used to achieve sleep deprivation, animals were monitored continuously.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
In all experiments, control non-sleep deprived animals were sacrificed at the same time as experimental animals. Following sleep deprivation, hippocampi were dissected from experimental and control animals and flash frozen using dry ice. RNA was harvested using Trizol reagent.
Illumina TruSeq Stranded Total RNA with Ribo-Zero gold sample preparation kit for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Ribosome associated mRNA
|
| Data processing |
Sequencing data was processed with the reads trimmed, aligned and quantified according to the MUGQIC RNA-seq pipeline (bitbucket.org/mugqic/genpipes/src/master/pipelines/rnaseq).
Raw reads quality trimming and removing of Illumina adapters was performed using Trimmomatic v0.36 with parameters ILLUMINACLIP:adapters-truseq.fa:2:30:15:8:true TRAILING:30 MINLEN:32
The remaining reads were then aligned to the Mus musculus reference genome (mm10) with STAR v2.7.5
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrix for all the samples was generated using HTSeq-counts in txt format
|
| |
|
| Submission date |
Aug 26, 2020 |
| Last update date |
Aug 27, 2020 |
| Contact name |
Yann Vanrobaeys |
| E-mail(s) |
yann-vanrobaeys@uiowa.edu
|
| Phone |
5059139210
|
| Organization name |
University of Iowa
|
| Department |
Neuroscience
|
| Lab |
Ted Abel
|
| Street address |
2312 PBDB, 169 Newton Road
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE156925 |
TRAP-Seq uncovers post-transcriptional gene regulation after acute sleep deprivation |
|
| Relations |
| BioSample |
SAMN15905550 |
| SRA |
SRX9008900 |
