|
| Status |
Public on Jul 12, 2012 |
| Title |
blood-pdc-2 |
| Sample type |
RNA |
| |
|
| Source name |
healthy donor, plasmacytoid dendritic cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: plasmacytoid dendritic cell
cell subtype: pDC
disease state: healthy
|
| Treatment protocol |
None.
|
| Growth protocol |
Monocytes and dendritic cell subsets were purified by FACS sorting from primary samples for transcription analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from monocytes using an RNeasy Mini Kit (Qiagen) as per manufacturer's specifications. Extracted RNA was runned and quantified on a Bioanalyser (Agilent) for quality control and used subsequently in a microarray assay.
|
| Label |
biotin
|
| Label protocol |
Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).
|
| |
|
| Hybridization protocol |
According to BeadChip array manufacturer's protocol.
|
| Scan protocol |
According to BeadChip array manufacturer's protocol.
|
| Description |
BD_pDC_II
healthy donor, plasmacytoid dendritic cell,Homo sapiens,blood,plasmacytoid dendritic cell,pDC,total RNA,biotin
|
| Data processing |
Array data were extracted at the probeset level with no background correction using Illumina's BeadStudio software. These raw data were normalised using the Loess method within the LUMI package in R/Bioconductor v2.13.1. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate, and probesets with corrected p-value less than 0.05 were considered.
|
| |
|
| Submission date |
Jan 31, 2012 |
| Last update date |
Oct 23, 2015 |
| Contact name |
Pavandip Singh Wasan |
| E-mail(s) |
pavandip_wasan@immunol.a-star.edu.sg
|
| Organization name |
Singapore Immunology Network
|
| Department |
Bioinformatics
|
| Street address |
8A Biomedical Grove, #03-06, Immunos
|
| City |
Singapore |
| ZIP/Postal code |
138648 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE35457 |
Transcriptome profiles of mouse and human monocyte and dendritic cell subsets (human data) |
| GSE35459 |
Transcriptome profiles of mouse and human monocyte and dendritic cell subsets |
|
| Relations |
| Reanalyzed by |
GSE74316 |
