|
| Status |
Public on Feb 01, 2018 |
| Title |
SOD1 1 |
| Sample type |
SRA |
| |
|
| Source name |
Human neuroblastoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
neuroblastoma cell line: SHSY-5Y
genotype/variation: wild type SOD1
|
| Treatment protocol |
none
|
| Growth protocol |
SH-SY5Y cells, either untransfected or stably transfected with cDNAs coding for wild type SOD1 or the mutant SOD1(G93A) were cultured in D-MEM high glucose medium, 10% fetal bovine serum (FBS), 2.5 mM L-glutamine, 100 U/ml penicillin, and 100 µg/ml streptomycin (all products were purchased by Euroclone) at 37°C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions.
Enriched RNA samples were processed using the Small RNA Expression Kit according to the manufacturer’s protocol (Small RNA expression kit, rev. C, Applied Biosystems). RNA was first hybridized and ligated with the adapter mix “A”, subsequently reverse transcribed and treated with RNAse H. The obtained cDNA libraries were PCR amplified, purified and size-selected by PAGE, resulting in libraries containing inserted small RNA sequences of 20–40 bp length. Size, integrity and purity of the libraries were verified by the Agilent 2100 Bioanalyzer (Agilent Technologies). cDNA libraries were barcoded using the Solid RNA barcoding kit and amplified onto beads using emulsion PCR.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Data processing |
Reads were trimmed to have a length of 25 nts
Genome_build: miRBase v19.0
|
| |
|
| Submission date |
Feb 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Raffaele A Calogero |
| E-mail(s) |
raffaele.calogero@unito.it
|
| Phone |
++39 0116706454
|
| Organization name |
University of Torino
|
| Department |
Molecular Biotechnology Center
|
| Lab |
Bioinformatics and Genomics Unit
|
| Street address |
Via Nizza 52
|
| City |
Torino |
| State/province |
To |
| ZIP/Postal code |
10126 |
| Country |
Italy |
| |
|
| Platform ID |
GPL13393 |
| Series (1) |
| GSE94379 |
MiR-129-5p downregulates HuD expression impairing neuritogenesis in Amyotrophic Lateral Sclerosis |
|
| Relations |
| BioSample |
SAMN06288351 |
| SRA |
SRX2532214 |
