|
| Status |
Public on May 06, 2018 |
| Title |
Control1_crush |
| Sample type |
SRA |
| |
|
| Source name |
Sciatic nerve
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Sciatic nerve
strain: C57BL/6
age: 5 days post-crush
genotype: Control
surgery: Injured
|
| Treatment protocol |
Sciatic nerves surgeries were performed 2 months after the last tamoxifen injection
|
| Growth protocol |
Controls and mutants were injected with tamoxifen at 2 months of age
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nerves were extracted, flash frozen in liquid nitrogen after mechanical removal of the epineurium, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
adapter sequences were removed, low quality ends trimmed, and reads with low quality (phred quality<20) filtered using Trimmomatic (Bolger et al., Bioinformatics, 2014)
high-quality reads were mapped to the mouse reference genome and quantification of gene level expression was carried out using RSEM (version 1.2.22)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for each sample
|
| |
|
| Submission date |
Dec 18, 2017 |
| Last update date |
May 06, 2018 |
| Contact name |
Gianluca Figlia |
| E-mail(s) |
gianluca.figlia@biol.ethz.ch
|
| Organization name |
ETH Zurich
|
| Department |
Institute for Molecular Health Sciences
|
| Lab |
Suter lab
|
| Street address |
Otto-Stern-Weg 7
|
| City |
Zurich |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE108231 |
RNA sequencing of control and raptor-knockout mouse sciatic nerves after crush injury |
|
| Relations |
| BioSample |
SAMN08200070 |
| SRA |
SRX3480676 |
