|
| Status |
Public on May 20, 2024 |
| Title |
3-3JEVControl6hpi_R1 |
| Sample type |
SRA |
| |
|
| Source name |
N9
|
| Organism |
Mus musculus |
| Characteristics |
cell line: N9
cell type: Microglia
treatment: JEV infection
time point: 6h
|
| Treatment protocol |
N9 cells were pretretaed with SCFA cocktail for 12 hours, followed by 2hrs serum starvation and incubation in JEV containing medium for 2 hrs. Thereafter the cells were transferred to mainatence media and collected 6 hours and 24 hours post infection.
|
| Growth protocol |
N9 microglial cells were grown and maintained in DMEM substituted with 10% FBS and 100units/mL of penstrap in humidified atmosphere at 37 degrees celcius and 5% CO2
|
| Extracted molecule |
other |
| Extraction protocol |
Total RNA was extracted using phenol-chloroform method The RNA pellet was dissolved in RNase free water and rRNA depletion was performed using 1 μg of total RNA and further used for library preparation.
NEBNext® Ultra™ II Directional RNA Library Prep Kit was used to prepare RNA-seq libraries according to manufacturer's protocol
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
other |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Quality check of the data was performed using FastQC v0.11.9 and MultiQC v1.9 software.
Trimgalore v0.6.6 and Cutadapt v3.4 programs were used to remove adaptor sequencesand low quality bases
sequencing data were mapped onto indexed Mouse reference genome (GRCm38) using mapper.pl script of miRDeep2 v2.0.1.2.
Assembly: GRCm38
Supplementary files format and content: Expression counts and normalized expression counts in xlsx files
|
| |
|
| Submission date |
May 10, 2024 |
| Last update date |
May 20, 2024 |
| Contact name |
Anirban Basu |
| E-mail(s) |
anirban@nbrc.ac.in
|
| Organization name |
National Brain Research Centre
|
| Department |
Cellular and molecular neuroscience
|
| Street address |
Nainwal Mor, Manesar
|
| City |
Gurugram |
| State/province |
Haryana |
| ZIP/Postal code |
122052 |
| Country |
India |
| |
|
| Platform ID |
GPL15103 |
| Series (1) |
| GSE267173 |
Short-chain fatty acids abrogate Japanese encephalitis virus-induced inflammation in microglial cells via miR200a-3p/ZBTB20/Ikβα axis |
|
| Relations |
| BioSample |
SAMN41318359 |
| SRA |
SRX24516034 |
