|
Status |
Public on Mar 06, 2023 |
Title |
CW605-2 |
Sample type |
SRA |
|
|
Source name |
Brain
|
Organism |
Mus musculus |
Characteristics |
tissue: Brain cell type: BCECs genotype: WT treatment: 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 |
X11514
|
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 |
SAMN31621973 |
SRA |
SRX18180105 |