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Sample GSM3427042 Query DataSets for GSM3427042
Status Public on Oct 12, 2018
Title A549 cells infected by Influenza virus PR8 replicate 3
Sample type SRA
 
Source name A549 cells
Organism Homo sapiens
Characteristics cell line: A549
cell type: Adenocarcinomic lung epithelial cells
gender: male
treatment: Influenza virus PR8 infection
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from A549 cells by using Tri Reagents.
Libraries were prepared with the Illumina TruSeq Stranded mRNA Library Preparation kit. Briefly, poly-adenylated mRNA were selected using oligo-dT beads and fragmented to 300-500bp. Each fragment undergoes cDNA synthesis using random hexamer. Indexed adapters were ligated to the resulting cDNA.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Flu3
Data processing The indexed libraries were pooled in equal molar ratio and sequenced on the Illumina NextSeq 500 system using 2x75bp paired-end sequencing.
Paired-end reads were directionally mapped to the genomic loci of lncRNA (GRCh37 /hg19) by TopHat2.
Cufflinks/Cuffdiff analysis was run to identify the dysregulated RNAs.
Genome_build: GRCh37 /hg19
Supplementary_files_format_and_content: *.fpkm_tracking: Tab-delimited text files include FPKM values generated by Cufflinks.
 
Submission date Oct 11, 2018
Last update date Oct 12, 2018
Contact name CHAOQUN HUANG
E-mail(s) chaoqh@okstate.edu
Phone 405-744-3410
Organization name Oklahoma State University
Department Physiological Sciences
Lab Lundberg-Kienlen Lung Biology and Toxicology Laboratory
Street address 264 McElroy Hall
City Stillwater
State/province OK
ZIP/Postal code 74078
Country USA
 
Platform ID GPL18573
Series (1)
GSE121155 Effect of Influenza virus infection on lncRNA expression in A549 cells
Relations
BioSample SAMN10233010
SRA SRX4867902

Supplementary file Size Download File type/resource
GSM3427042_genes_fpkm_Flu3.fpkm_tracking.gz 1.8 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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