|
| Status |
Public on Apr 30, 2012 |
| Title |
Monocyte RNA 6h X4300799014_G_t1 |
| Sample type |
RNA |
| |
|
| Source name |
Monocyte
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: monocyte
stage of mi infection: 6h
age: 71
gender: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolation of monocytes was performed by an immuno-magnetic method using the Miltenyi AutoMacs cell separator using whole-blood CD14+ beads (Miltenyi) according to the manufacturers’ instructions
|
| Label |
biotin-16-UTP
|
| Label protocol |
In vitro transcription reaction of cDNA to cRNA was performed overnight at 37°C including biotin-16-UTP for labelling
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina hybridization protocol
|
| Description |
Monocyte RNA 6h
replicate 1 time point t1 (6h)
|
| Data processing |
Quality control, background correction, variance stabilization (Lin et al. 2008) and normalization were performed in R statistical environment using the Lumi package (Du et al. 2008). Briefly, output from Illumina’s Bead Studio software (BeadStudio User Guide. San Diego, USA 2004; 2005. http://www.illumina.com) was downloaded into R and a series of quality control and diagnostics were performed to assess the quality of raw and normalized data. Background correction was performed using the Illumina’s default algorithm which uses the signals from negative control bead types to estimates the expected background signal levels. After background correction and filtering out array outliers, variance stabilization transformation (VST) was performed on the intensity data. Data were normalized using quantile normalization method (Bolstad et al. 2003) to make the same overall distribution of expression intensities for all the arrays within the experiment. Control probes as well as transcripts absent (not expressed) in all samples were filtered out (a detection P-value < 0.01 was used as a threshold).
|
| |
|
| Submission date |
Apr 07, 2011 |
| Last update date |
Apr 30, 2012 |
| Contact name |
Heribert Schunkert |
| E-mail(s) |
Heribert.Schunkert@uk-sh.de
|
| Phone |
00494515002501
|
| Fax |
00494515006337
|
| URL |
http://www.innere2-luebeck.uk-sh.de
|
| Organization name |
Universitaetsklinikums Schleswig-Holstein Luebeck
|
| Department |
Medizinische Klinik II
|
| Lab |
Cardiovacsular genomics
|
| Street address |
Ratzeburger Allee 160
|
| City |
Luebeck |
| ZIP/Postal code |
D-23538 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6883 |
| Series (1) |
| GSE28454 |
Temporal transcriptional changes in human monocytes following acute myocardial infarction: The GerMIFs monocyte expression study |
|
