|
Status |
Public on Aug 11, 2009 |
Title |
P19t2 |
Sample type |
RNA |
|
|
Source name |
Monocyte from patient, 2wk EPO
|
Organism |
Homo sapiens |
Characteristics |
patient number: 19 disease: cardiorenal syndrome (CRS) cell type: monocyte timepoint (weeks): 2 age: 52 gender: F treatment group: EPO, may rise in hemoglobin levels
|
Growth protocol |
Monocytes were positively isolated from whole blood by CD14+ immunomagnetic beads (Dynabeads, Invitrogen, Carlsbad, CA). Cells were directly lysed and stored.
|
Extracted molecule |
total RNA |
Extraction protocol |
mRNA was isolated from monocytes using Trizol reagent (Invitrogen/Gibco, USA) according to the manufacturer’s instruction. Subsequently, mRNA was purified with NucleoSpin® RNA II (Macherey-Nagel, Düren, Germany).
|
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 |
372-47
|
Data processing |
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e. mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray) after log2-transformation. P-value <0.05 was considered significant.
Non-normalized data are available in the 'GSE17582_non-normalized_data.txt' file, which is linked to the Series GSE17582 record as a supplementary file.
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|
|
Submission date |
Aug 10, 2009 |
Last update date |
Aug 11, 2009 |
Contact name |
Branko Braam |
E-mail(s) |
bbraam@gmail.com
|
Phone |
780 407 3322
|
Fax |
780 407 7771
|
URL |
http://www.nephrogenomics.net
|
Organization name |
Univ. of Alberta
|
Department |
Medicine / Nephrology
|
Street address |
11-107 CSB
|
City |
Edmonton |
ZIP/Postal code |
T6C 3X6 |
Country |
Canada |
|
|
Platform ID |
GPL6883 |
Series (1) |
GSE17582 |
Effect of two weeks erythropoietin treatment on monocyte transcriptomes of cardiorenal patients |
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