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Sample GSM3487604 Query DataSets for GSM3487604
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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