|
| Status |
Public on Dec 08, 2022 |
| Title |
1_4003.sample |
| Sample type |
SRA |
| |
|
| Source name |
NestinTK+ GCV
|
| Organism |
Mus musculus |
| Characteristics |
cell type: neural precursor cells from SVZ
strain: C57Bl/6
tissue: brain
genotyping: NestinTK
treatment: Ganciclovir
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SVZ and striatum were removed, flash frozen on dry ice, and RNA was harvested using Rnase Mini Kit (Qiagen Cat No./ID: 74106)
For SVZ tissue libraries were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA) performing 10 cycles of amplification, according to the manufacturer’s instructions, while for the striatum tissue libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.36)
Retained reads were mapped to the reference mouse genome GRCm38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts function in the Rsubread R package. Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode v. M13 for the striatum tissue; Gencode v. M16 for the SVZ tissue)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jan 29, 2021 |
| Last update date |
Dec 08, 2022 |
| Contact name |
Giulia Maria Scotti |
| E-mail(s) |
giulis.scotti@gmail.com
|
| Organization name |
Fondazione Human Technopole
|
| Department |
National Facility for Data Handling and Analysis
|
| Street address |
Viale Rita Levi Montalcini, 1
|
| City |
Milan |
| State/province |
Milan |
| ZIP/Postal code |
20157 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE165815 |
Neural precursor cells contribute to decision-making by tuning striatal connectivity via secretion of IGFBPL-1 |
|
| Relations |
| BioSample |
SAMN17696092 |
| SRA |
SRX9977787 |
