|
| Status |
Public on Mar 14, 2014 |
| Title |
MAC_CONTROL |
| Sample type |
SRA |
| |
|
| Source name |
monocyte-derived macrophages_mock infected
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: monocyte-derived macrophages
|
| Treatment protocol |
Human peripheral blood mononuclear cell-derived macrophages were infected with HRV16, HRV1A, or mock at an MOI of 10 for 8 hours.
|
| Growth protocol |
Human peripheral blood monocytes were cultured in RPMI 1640 (Cellgro) with 5% human AB serum (Cellgro, Manassa, VA) and 1% penicillin/streptomycin (Gibco) at 37˚C in a humidified incubator with 5% CO2. THP-1 monocytes were cultured in RPMI1640 with 5% fetal calf serum (HyClone) and 1% Penicillin/Streptomycin. For infectious center assay experiments, cells were plated at 7.5 X 10^5 cells / well in 2 mL of cell culture medium to 6-well plates (BD Falcon). To induce THP1 differentiation to monocyte-derived macrophages, cells were treated for 24 hr with phorbol myristate acetate (PMA) (Fisher Scientific) at a concentration of 200 nM. Following the differentiation, the PMA-containing medium was removed and replaced with an equal volume of fresh medium, and the cells were rested for an additional 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed 5x in PBS, and RNA was harvested by extraction with Trizol and purified by RNeasy column elution. RNA quality was ensured by Agilent Bioanalyzer 2100 analysis.
RNA samples were submitted to the Columbia Genome Center for stranded ribominus library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Data processing |
Sequencing reads were trimmed to 36 base pairs and mapped against the reference genome (hg19 assembly) using the BWA. Only uniquely placed reads were used for further analysis.
Cisgenome v2.0 was used to calculate reads per 1000 base pairs of transcript per million reads sequenced (RPKM) values for all RefSeq annotated transcripts. To avoid transcripts with zero mapped tags to interfere with logarithmic transformation of read counts, 0.1 read was added to each transcript. Raw read counts were normalized to the transcript length and sequencing depth and quantile normalized
Genome_build: hg19
Supplementary_files_format_and_content: *.rna files were generated using Cisgenome “rnaseq_countgeneread” command
|
| |
|
| Submission date |
Feb 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michal Mokry |
| E-mail(s) |
m.mokry@umcutrecht.nl
|
| Organization name |
Wilhelmina Children's Hospital, University Medical Center Utrecht
|
| Street address |
Lundlaan 6
|
| City |
Utrecht |
| ZIP/Postal code |
3584 EA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL15433 |
| Series (1) |
| GSE55271 |
Major and Minor Group Human Rhinovirus Response in Human Macrophages |
|
| Relations |
| BioSample |
SAMN02649578 |
| SRA |
SRX474875 |
