|
| Status |
Public on Oct 03, 2017 |
| Title |
TBI subacute 3 |
| Sample type |
SRA |
| |
|
| Source name |
Brain Endothelial cells
|
| Organism |
Mus musculus |
| Characteristics |
disease model: TBI
timepoint: Subacute
|
| Growth protocol |
FACS purification of endothelial cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS purification of endothelial cells into Trizol. Phenol chloroform extraction was used to isolate RNA
Prepared at the Gladstone Genomics core: NuGEN Ovation RNA-seq V2 kit and NuGEN Ovation Ultralow kit wereused
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Raw_per-gene_counts_AS-522.txt.gz
|
| Data processing |
Alignment: Aligned to mouse genome build "mm9" using the program Tophat 2.0.13. Gene annotation (GTF file) used was Ensembl version 65. Specific settings: --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --microexon-search --mate-inner-dist=150 --no-discordant --no-mixed
Reads to gene-level counts: Aligned reads were assigned to genes to arrive at per-gene counts using "featureCounts" (Liao et al., 2014), part of the Subread suite (http://subread.sourceforge.net/).
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: Raw per-gene count data table in plain text format, suitable for loading in Excel
|
| |
|
| Submission date |
Feb 27, 2017 |
| Last update date |
Jan 14, 2020 |
| Contact name |
Roeben Munji |
| E-mail(s) |
rmunji@health.ucsd.edu
|
| Organization name |
University of California San Diego
|
| Department |
Pharmacology
|
| Lab |
Richard Daneman
|
| Street address |
9500 Gilman Dr.
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE95401 |
The cerebrovascular response to injury and disease |
|
| Relations |
| SRA |
SRX2594692 |
| BioSample |
SAMN06472519 |
