|
| Status |
Public on Jun 18, 2021 |
| Title |
WT ipsi MB aSyn SAM24372733 |
| Sample type |
SRA |
| |
|
| Source name |
RNA from brain region tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
genotype: WT
side: ipsilateral
region: midbrain
aav: aSyn-A53T
samid: SAM24372733
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissue was rapidly frozen and stored until a full collection was obtained. RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.
|
| |
|
| Submission date |
Dec 20, 2020 |
| Last update date |
Jun 18, 2021 |
| Contact name |
Brad A Friedman |
| E-mail(s) |
friedmab@gene.com
|
| Organization name |
Genentech, Inc.
|
| Department |
Bioinformatics
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94133 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE163559 |
Role of Gpnmb in response to virally expressed mutant SNCA |
|
| Relations |
| BioSample |
SAMN17124429 |
| SRA |
SRX9707753 |
