|
| Status |
Public on Oct 12, 2018 |
| Title |
A549 cells treated with PBS 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: Mock 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 |
Control3
|
| 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 |
SAMN10233013 |
| SRA |
SRX4867899 |
