|
Status |
Public on Nov 24, 2018 |
Title |
Virus_1 |
Sample type |
SRA |
|
|
Source name |
Calu-3 cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: Calu-3 cell type: lung adenocarcinoma passage: 9
|
Treatment protocol |
Calu-3 cells were mock infected or infected with MERS-CoV at 2 MOI and incubated in DMEM medium. At 24hpi, total cellular RNAs were collected.
|
Growth protocol |
Cells are maintained in DMME medium supplemented with 10% heat-inactivated Fetal Bovine Serum (FBS) (Gibco), 50 units/ml penicillin and 50 µg/ml streptomycin (P/S) (Invitrogen)
|
Extracted molecule |
total RNA |
Extraction protocol |
Cell lysate were collected and cellular RNA were extracted using Rneasy mini rna extraction kit (qiagen) RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
BGISEQ-500 |
|
|
Data processing |
BGISeq-500 reads were trimmed and clipped for quality control. Read quality was checked for each sample using FastQC v0.10.1. High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files. BAM files were imported into Cufflinks v2.0.2 for FPKM count and DEG analysis. Genome_build: hg19 Supplementary_files_format_and_content: FPKM of all genes in all conditions in xls format
|
|
|
Submission date |
Nov 23, 2018 |
Last update date |
Nov 26, 2018 |
Contact name |
Shuofeng Yuan |
E-mail(s) |
yuanshuofeng@gmail.com
|
Organization name |
The University of Hong Kong
|
Department |
Microbiology
|
Street address |
Block T, 122 Pokfield Road Sai Wan
|
City |
Hong Kong |
State/province |
Hong Kong |
ZIP/Postal code |
999077 |
Country |
Hong Kong |
|
|
Platform ID |
GPL23227 |
Series (1) |
GSE122876 |
Transcriptomic analysis of MERS-CoV infected Calu-3 cell with or without AM580 treatment |
|
Relations |
BioSample |
SAMN10473212 |
SRA |
SRX5058253 |