|
| Status |
Public on May 20, 2024 |
| Title |
Cerebral cortex, 7days after ZIKV infection, Bio rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Cerebral cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Cerebral cortex
strain: A129
Sex: Female
genotype: IFN-a/b receptor knockout
treatment: ZIKV-FLR infection
time: 7days post-infection
|
| Treatment protocol |
The experimental group was intraperitoneally injected with either ZIKV-FLR strain at a concentration of 5 × 10^4 PFU/ml, while the uninfected control group was intraperitoneally injected with an equivalent volume of PBS. Mice were monitored daily for signs of illness, including changes in body weight and mortality
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using the PureLink™ RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina NovaSeq 6000
Sequenced RNA-sequencing reads were trimmed for adapter seuquence, and processed for eliminating artifacts such as contaminant DNA or PCR duplicates using Trimmomatic 0.38 with parameters SLIDINGWINDOW:4:15 TRAILING:3 LEADING:3 MINLEN:36.
Trimmed reads were mapped to reference genome (UCSC GRCm38/mm10) using the Bowtie2 2.3.4.1 aligner.
Fragments per kilobase of transcript per million mapped reads (FPKM) was estimated with StringTie for mus musculus genes.
Assembly: mm10
Supplementary files format and content: GTF file contains the merged transcript annotations generated using StringTie
|
| |
|
| Submission date |
Apr 25, 2024 |
| Last update date |
May 20, 2024 |
| Contact name |
Nahyun Kim |
| E-mail(s) |
knh64@naver.com
|
| Organization name |
Konkuk university
|
| Street address |
120 Neungdong-ro, Gwangjin-gu, Seoul
|
| City |
Seoul |
| ZIP/Postal code |
05025 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE265861 |
Analysis of Gene Expression in the Recovered Mouse Brain following Zika Virus Infection |
|
| Relations |
| BioSample |
SAMN41085502 |
| SRA |
SRX24373000 |
