|
| Status |
Public on Apr 10, 2013 |
| Title |
Uncultured monocyte-enriched PBMCs, sample 3 |
| Sample type |
RNA |
| |
|
| Source name |
PBMCs, uncultured
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: monocyte-enriched peripheral blood mononuclear cells
developmental stage: adult
Stage: uncultured
donor: 3
|
| Treatment protocol |
None
|
| Growth protocol |
PBMCs were subjected to cold-aggregation for monocyte-enrichment and cultured in standard culture conditions with RPMI with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA is extracted by RNAzol.
|
| Label |
biotin
|
| Label protocol |
500ng total RNA is converted to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Ambion, Inc.) as per manufacturer's instructions.
|
| |
|
| Hybridization protocol |
750ng of the labeled probes are then mixed with hybridization reagents and hybridized overnight at 58°C to the HT-12 v4 BeadChips.
|
| Scan protocol |
Following washing and staining with Cy3-streptavidin conjugate, the BeadChips are imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe.
|
| Description |
2901 agg 9-14
|
| Data processing |
The background corrected gene expression levels were extracted from BeadChip using Illumina's Genome Studio (v2011.1) gene expression module (v1.9.0). The log2 transformed expression levels were quantile normalized using Lumi module in the R-based Bioconductor package.
|
| |
|
| Submission date |
Apr 09, 2013 |
| Last update date |
Apr 10, 2013 |
| Contact name |
Biao Liu |
| E-mail(s) |
biao.liu@roswellpark.org
|
| Organization name |
Roswell Park Cancer Institute
|
| Department |
Center for Personalized Medicine
|
| Street address |
Elm and Carlton streets
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE45900 |
Characterizing gene expression changes that accompany succinate dehydrogenase subunit B (SDHB) RNA editing in monocyte-enriched peripheral blood mononuclear cell cultures |
|
