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Sample GSM438059 Query DataSets for GSM438059
Status Public on Aug 11, 2009
Title GZ25t0
Sample type RNA
 
Source name Monocyte from healthy control
Organism Homo sapiens
Characteristics patient number: Healthy25
disease: healthy
cell type: monocyte
timepoint (weeks): 0
age: 40
gender: M
treatment group: Healthy controls
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 372-07
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.
 
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

Data table header descriptions
ID_REF
VALUE Quantile-normalized signal intensity

Data table
ID_REF VALUE
ILMN_1343291 44188.09
ILMN_1651209 83.07
ILMN_1651228 4141.94
ILMN_1651229 123.09
ILMN_1651235 73.07
ILMN_1651236 90.05
ILMN_1651237 76.31
ILMN_1651238 69.75
ILMN_1651254 307.22
ILMN_1651260 68.54
ILMN_1651262 1861.15
ILMN_1651268 97.98
ILMN_1651278 133.72
ILMN_1651282 84.01
ILMN_1651285 66.18
ILMN_1651286 137.74
ILMN_1651292 54.55
ILMN_1651303 81.65
ILMN_1651309 77.51
ILMN_1651315 509.68

Total number of rows: 24526

Table truncated, full table size 466 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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