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Sample GSM8261829 Query DataSets for GSM8261829
Status Public on May 20, 2024
Title 4-6SCFAControl24hpi_R1
Sample type SRA
 
Source name N9
Organism Mus musculus
Characteristics cell line: N9
cell type: Microglia
treatment: SCFA cocktail
time point: 12h
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 SAMN41318348
SRA SRX24516045

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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