|
| Status |
Public on Oct 01, 2018 |
| Title |
Silc1 KO brain 2 |
| Sample type |
SRA |
| |
|
| Source name |
Adult brain
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Silc1 KO
|
| Treatment protocol |
Mice were anesthetized with an intraperitoneal injection of xylazine and ketamine (10 mg/kg body weight). A 1-cm-long incision was made in the skin of the thigh perpendicular to the femur. A small incision was made between the thigh muscles and the muscles were separated by insertion and opening of the tip of the scissors between the muscles. The sciatic nerve was identified and pulled out using 45º forceps. The tissue was crushed using fine forceps (Dumont no. 4) two times for 30 seconds at mid- thigh level. The sciatic was positioned back in its place by gently pooling the hind leg. The incision was closed using reflex wound clips. Adult mouse DRGs were dissociated for neuron cultures with 100 U of papain followed by 1 mg/ml collagenase-II and 1.2 mg/ml dispase. The ganglia were then triturated in HBSS, 10 mM glucose, and 5 mM HEPES (pH 7.35). Neurons were recovered through percoll, plated on laminin, and grown in F12 medium for 48 hours (Hanz et al., 2003; Perlson et al., 2005; Rishal et al., 2010). Adult mouse DRG cultures were transfected with siGenome siRNAs using DharmaFect 4 (Dharmacon), replated 24 hr later
|
| Growth protocol |
The study was conducted in accordance with the guidelines of the Weizmann Institutional Animal Care and Use Committee (IACUC). C57black6 Ola HSD male mice were purchased from Harlan Laboratories (Rehovot, Israel). All other mouse strains were bred and maintained at the Veterinary Resources Department of the Weizmann Institute.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from total DRGs pooled from 3 animals, using the Trizol reagent (TRI, Sigma-Aldrich) according to the manufacturer’s protocol.
TruSeq stranded mRNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quantification using RSEM
Alignment to the mm10 mouse genome using STAR2
Preparation of bigWig files using wigToBigWIg
Genome_build: mm10
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage
|
| |
|
| Submission date |
Mar 06, 2018 |
| Last update date |
Oct 01, 2018 |
| Contact name |
Igor Ulitsky |
| E-mail(s) |
igor.ulitsky@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Street address |
Hertzl St.
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE111497 |
Regulation of neuroregeneration by long noncoding RNAs [RNA-seq] |
| GSE119491 |
Regulation of neuroregeneration by long noncoding RNAs |
|
| Relations |
| BioSample |
SAMN08640472 |
| SRA |
SRX3769001 |
