NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1387923 Query DataSets for GSM1387923
Status Public on Jun 10, 2014
Title SARS_MRC5lowMOI_24hr_2
Sample type SRA
 
Source name MRC5 Cell Line
Organism Homo sapiens
Characteristics cell line: MRC5
Treatment protocol RNA was isolated at 24 and 48 hours post infection at an MOI of 0.1 and 3 with each virus.
Growth protocol MRC5 cells were grown in MEM with 10% Fetal Bovine Serum
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol from cells infected in culture.
Poly-A RNA was isolated and indexed libraries were prepared for sequencing using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome reference build GRCh37.74 using bowtie v0.12.9 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37.74
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
 
Submission date May 16, 2014
Last update date May 15, 2019
Contact name David A Rasko
E-mail(s) drasko@som.umaryland.edu
Phone 410 706 6774
Organization name University of Maryland School of Medicine
Department Istitute for Genome Sciences/Microbiology and Immunology
Street address 801 W. Baltimore Street, Room 619
City Baltimore
State/province MD
ZIP/Postal code 21201
Country USA
 
Platform ID GPL11154
Series (2)
GSE56189 Transcriptomic Analysis Of The Novel Middle East Respiratory Syndrome Coronavirus (MERS-CoV)
GSE56192 Transcriptomic analysis of the Novel Middle East Respiratory Syndrome Coronavirus (Human, MRC5 cells)
Relations
BioSample SAMN02689265
SRA SRX490346
SRA SRX490347
SRA SRX490348

Supplementary file Size Download File type/resource
GSM1387923_SARS_MRC5LowMOI_24hr_2.rpkm.txt.gz 1.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap