|
| Status |
Public on Oct 01, 2023 |
| Title |
MB_OLD_WT_MALE_C3.10_ONT |
| Sample type |
SRA |
| |
|
| Source name |
ventral midbrain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: ventral midbrain
cell type: dopaminergic neurons
region: MB
age: OLD
genotype: WT
Sex: MALE
collection: C3.10
|
| Treatment protocol |
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
|
| Growth protocol |
C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Data processing |
Reads were trimmed using trim galore with default settings
Alignment and quantification were performed using Salmon in mapping mode, using Gencode mm10 genome/transcriptome data as a reference
Read count extraction and normalization were performed using tximeta and DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts values for each sample
|
| |
|
| Submission date |
Oct 11, 2022 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Peter Kilfeather |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oxford
|
| Department |
Department of Physiology, Anatomy and Genetics
|
| Lab |
Wade-Martins Laboratory of Molecular Neurodegeneration
|
| Street address |
Biochemistry Building Phase II, South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3QU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24973 |
| Series (1) |
| GSE215276 |
Translating ribosome affinity purification analysis of dopaminergic neurons of the mouse ventral midbrain with age and alpha-synuclein overexpression. |
|
| Relations |
| BioSample |
SAMN31247319 |
| SRA |
SRX17853917 |
