|
Status |
Public on Mar 06, 2023 |
Title |
OB 607-3 [X11527] |
Sample type |
SRA |
|
|
Source name |
Brain
|
Organism |
Mus musculus |
Characteristics |
tissue: Brain strain: C57BL/6 cell type: olfactory bulb BCECs genotype: WT treatment: Mock
|
Treatment protocol |
Control: Mock inoculated mice C57BL/6 weanling mice were infected with a 2000 PFU IP dose of LACV diluted into 200ul of sterile, pharmaceutical grade PBS. Mock mice received an equivalent volume of uninfected Vero supernatant diluted in PBS
|
Growth protocol |
OB and CT BCECs were isolated ex vivo after 3 days from weanling mice infected with La Crosse virus (2000PFU/mouse, intraperitoneal) or mock inoculated (200ul/mouse)
|
Extracted molecule |
polyA RNA |
Extraction protocol |
RNA was harvested using RNA isolation kit (Zymo Research). 170ng 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 |
|
|
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 07, 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) |
GSE217433 |
Comparison of weanling obfactory bulb (OB) and cortical (CT) brain capillary endothelial cells (BCECs) with or without La Crosse Virus infection |
GSE217434 |
Identification of age-specific gene regulators of La Crosse virus neuroinvasion and Pathogenesis. |
|
Relations |
BioSample |
SAMN31636234 |
SRA |
SRX18192649 |