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Sample GSM3729209 Query DataSets for GSM3729209
Status Public on Jul 27, 2020
Title miR-NC1-replicate1
Sample type SRA
 
Source name A549_miR-NC1
Organism Homo sapiens
Characteristics cell line: A549
transfection: miR-NC1
infection: Newcastle Disease Virus (NDV)
Treatment protocol Transfection: Cells were transfected with miR-NC1 or miR-30e mimic using Lipofectamine 2000 reagent.
Infection: Cell monolayer were washed with PBS and infected with 5 MOI of NDV virus for 1 hour in serum free DMEM. Cells were washed again with PBS and cultured in DMEM supplemented with 1% FBS after infection.
Growth protocol A549 cells were cultured in DMEM media supplemented with 10% FBS in 100 mm cell culture dishes. For transfection and infection cells were cultures in a 6 well cell culture plate.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with the help of Trizol reagent (Invitrogen)
Library was constructed with the help of Illumina TruSeq library preparation kit v2.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing FastQC was used to assess the quality of reads.
Trimmomatic was used for filtering and trimming of bad quality reads and sequences.
HISAT2 was used to map reads to human genome (hg38).
StringTie was used for transcript assembly and generation of abundance files.
DESeq2 R package was used for Differential Expression analysis and various R packages were used for generation of different plots and heat maps.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files containg not normalized (raw) read counts for each gene.
 
Submission date Apr 18, 2019
Last update date Jul 27, 2020
Contact name Himanshu Kumar
E-mail(s) hkumar@iiserb.ac.in
Organization name IISER Bhopal
Department Biological Sciences
Lab 215
Street address Indore bypass road
City Bhopal
State/province MADHYA PRADESH
ZIP/Postal code 462066
Country India
 
Platform ID GPL24676
Series (1)
GSE130005 Effect of miRNA-30e-5p on innate immunity during viral infection.
Relations
BioSample SAMN11461047
SRA SRX5707638

Supplementary file Size Download File type/resource
GSM3729209_miR_NC_1.txt.gz 239.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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