|
| Status |
Public on Jun 10, 2014 |
| Title |
MOCK_MRC5_Gleevec_24hrs |
| 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 2500 |
| |
|
| 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 |
GPL16791 |
| 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 |
SAMN02689149 |
| SRA |
SRX489366 |
| SRA |
SRX489367 |
| SRA |
SRX489368 |
| SRA |
SRX489369 |
| SRA |
SRX489370 |
| SRA |
SRX489371 |
| SRA |
SRX489372 |
| SRA |
SRX489373 |
