|
| Status |
Public on Mar 06, 2023 |
| Title |
CW575-1 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
cell type: BCECs
genotype: WT
treatment: Poly I:C-HMW/Lyovec (100ug/mouse)
|
| Treatment protocol |
Controls: Vehicle Lyovec-treated mice
|
| Growth protocol |
BCECs were isolated ex vivo after 3 hrs from mice treated with (retroorbital injection) vehicle or Poly I:C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
100ug of Poly(I:C) (HMW) diluted in a 0.5mg/mL LyoVec transfection reagent solution (Invivogen) via a 100ul retroorbital (IV) injection
RNA was harvested using RNA isolation kit (Zymo Research). 115ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
X11510
|
| Data processing |
Sequence reads were trimmed of adapter using cutadapt and trimmed and filtered for quality using FastX Toolkit
Trimmed reads were mapped to mm10 using hisat2
read count using htseq-count
data normalization and differential gene expression using deseq2
Assembly: mm10
Supplementary files format and content: tab delimited file containing deseq2 normalized read counts for each sample
|
| |
|
| Submission date |
Nov 06, 2022 |
| Last update date |
Mar 06, 2023 |
| Contact name |
Craig Martens |
| E-mail(s) |
martensc@niaid.nih.gov
|
| Phone |
406-363-9415
|
| Organization name |
NIAID
|
| Department |
DIR
|
| Lab |
RTB
|
| Street address |
903 S. 4th St
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE217382 |
Comparison of weanling and adult brain capillary endothelial cells (BCECs) with vehicle or Poly I:C treatment |
| GSE217434 |
Identification of age-specific gene regulators of La Crosse virus neuroinvasion and Pathogenesis. |
|
| Relations |
| BioSample |
SAMN31621977 |
| SRA |
SRX18180101 |
