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Sample GSM249444 Query DataSets for GSM249444
Status Public on Dec 18, 2007
Title BOEC, normal 20
Sample type RNA
 
Source name BOEC, normal 20
Organism Homo sapiens
Characteristics cell type: blood outgrowth endothelial cell
status: normal
race: Caucasian
age: 50
sex: F
Treatment protocol BOEC were always harvested at passage 3, which comprised a nominal million-fold expansion since establishing culture and amounted to ~3x107 BOEC. They were always harvested 4 hours after the last change of culture medium, and always when they were at 85-90% confluent.
Growth protocol We obtained citrated fresh peripheral blood (50-100 ml) from each donor. For donors outside the Minneapolis metropolitan area, blood was shipped by same-day express delivery in Saf-T-Pak cartons that had been pre-equilibrated to room temperature. Samples were processed immediately upon arrival at the University of Minnesota. Blood buffy coat mononuclear cells were prepared and cultured on rat collagen I, in presence of endothelial cell growth factors, as previous described in detail 15,16. All samples were handled identically
Extracted molecule total RNA
Extraction protocol We prepared BOEC lysates by adding 10 ml trizol (Gibco) to each T75 flask to solubilize the sample. As necessary, trizol lysates were stored in liquid nitrogen. We then isolated total RNA, and cleaned it using an RNeasy kit (Qiagen, CA).
Label biotin
Label protocol We used the Invitrogen SuperScript Choice system to reverse transcribe and synthesize double-stranded cDNA. For in vitro transcription and biotin-labeling, we synthesized biotin-labeled cRNA using the Enzo Life Sciences BioArray High Yield RNA Transcript Labeling kit. Then fragmentation of cRNA was done by standard protocol, and fragmentation was verified by gel electrophoresis.
 
Hybridization protocol After we prepared biotin-labeled cRNA fragments, samples were turned over immediately to our Microarray Core Facility which used Gene Chip Hybridization Oven 640, Affymetrix FS4000 Fluidics Station for staining with a streptavidin-fluorochrome probe and washing,
Scan protocol An Affymetrix High Resolution Scanner was used according to the manufacturer's standard manual
Description BOEC (blood outgrowth endothelial cells) from individuals that do not have sickle cell anemia
Data processing For raw microarray data, we used the RMA (robust multi-array average) method to summarize expression values from probe pair values; data were background-adjusted, quantile normalized (global scaling across multiple arrays). Expression measures were summarized based on log transformed PM (perfect match) values using Median Polish algorithm. Then, we used locally weighted scatterplot smoothing (LOWESS) to do within-array normalization. RMA and LOWESS were performed in Genedata Expressionist Pro3.1® (Basel, Switzerland).
 
Submission date Dec 13, 2007
Last update date Sep 01, 2016
Contact name Robert P. Hebbel
E-mail(s) enens001@umn.edu
Phone 612-6244620
Fax 612-625-8105
Organization name University of Minnesota
Department Medicine
Lab Vascular Biology Center
Street address MMC 480, 420 Delaware St. SE
City Minneapolis
State/province MN
ZIP/Postal code 55455
Country USA
 
Platform ID GPL96
Series (2)
GSE9877 Genetic Endothelial Systems Biology of Sickle Stroke Risk
GSE17078 Cell Adhesion Molecule 1 (CADM1): A Novel Risk Factor for Venous Thrombosis
Relations
Reanalyzed by GSE86363

Data table header descriptions
ID_REF
VALUE Expression measures were summarized based on log transformed PM (perfect match) values using Median Polish algorithm. Then, we used locally weighted scatterplot smoothing (LOWESS) to do within-array normalization. RMA and LOWESS were performed in Genedata Expressionist Pro3.1® (Basel, Switzerland).
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
221249_s_at 305.52936 0.001953125
211637_x_at 55.329365 0.93237305
219293_s_at 915.86285 2.44E-04
210348_at 55.12819 0.66552734
201532_at 859.5973 0.005859375
208769_at 163.50697 0.63378906
207765_s_at 297.5703 0.002929688
202862_at 157.40155 0.004150391
208846_s_at 453.72412 0.001953125
222362_at 142.78697 0.53393555
209927_s_at 158.29959 0.004150391
207104_x_at 142.20683 0.9538574
216251_s_at 332.23447 0.001220703
203776_at 242.85881 0.037597656
202787_s_at 151.08806 0.023925781
209438_at 113.73693 0.018554688
217466_x_at 2706.706 0.014160156
203868_s_at 289.16415 2.44E-04
202982_s_at 154.30835 0.1496582
205804_s_at 34.633163 0.9538574

Total number of rows: 22283

Table truncated, full table size 682 Kbytes.




Supplementary file Size Download File type/resource
GSM249444.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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