|
| Status |
Public on Aug 03, 2018 |
| Title |
visudyne_9 |
| Sample type |
SRA |
| |
|
| Source name |
Total RNA from hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Brain whole hippocampus
age: 2 months
genotype: Wild type
treatment: Visudyne
|
| Treatment protocol |
Intra-cisterna magna injection of Visudyne (verteporfin for injection), or vehicle as control, and photoconversion with 689-nm wavelength non-thermal red light above the intact skull. Procedure was repeated 2 weeks after.
|
| Growth protocol |
All C57BL/6J mice were bred and maintained in standard vivarium conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy mini kit (Qiagen)
The Illumina TruSeq Stranded Total RNA Library Prep Kit was used for cDNA library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
da_mesquita_visudyne_before_mwm_raw_counts.tsv
|
| Data processing |
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC.
Transcript-level abundances were calculated using Salmon.
Transcript-level abundances were summarized into gene-level counts with tximport.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file with the raw counts.
|
| |
|
| Submission date |
Apr 18, 2018 |
| Last update date |
Aug 03, 2018 |
| Contact name |
Christopher Overall |
| Organization name |
University of Virginia
|
| Department |
Neuroscience
|
| Street address |
409 Lane Road
|
| City |
Charlottesville |
| State/province |
Virginia |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE113351 |
Functional aspects of meningeal lymphatics in ageing and Alzheimer's disease [3 of 3] |
|
| Relations |
| BioSample |
SAMN08951005 |
| SRA |
SRX3963023 |
