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Sample GSM151635 Query DataSets for GSM151635
Status Public on Apr 01, 2011
Title ABI_Human Dermal Blood Vascular Endothelial Cells Donor 3
Sample type RNA
 
Source name Neonatal human foreskin
Organism Homo sapiens
Characteristics CD45-/CD34+ Human Blood Vascular Endothelial Cell (BVEC).
Extracted molecule total RNA
Extraction protocol Isolate total cellular RNA with 1 ml of the Trizol reagent (Invitrogen) after washing one 80-90 % confluent 10 cm culture dish with PBS. Homogenize the sample using a cell scraper and add 0.2 ml of chloroform in a 1.5 ml tube. Shake the sample vigorously for 15 seconds and allow standing for 5 minutes. Centrifuge the resulting mixture at 12,000 x g for 15 minutes at 4 degree Celsius. Transfer the aqueous phase to a fresh tube and add 0.5 ml of iso-propanol and mix. Allow the sample to stand for 5 minutes at room temperature and centrifuge at 12,000 x g for 10 minutes at 4 degrees Celsius. Remove the supernatant and wash the RNA pellet by adding 1 ml of 75% ethanol. Vortex the sample and then centrifuge at 12,000 x g for 5 minutes at 4 degrees Celsius. Remove the ethanol and briefly dry the RNA pellet for 5 minutes and add 50 micro-liter of RNAase/DNAase free water and mix by repeated pipetting until RNA pellet is fully dissolved.
Label Chemiluminescent Digoxigenin-UTP labeled cRNA
Label protocol Digoxigenin-UTP labeled cRNA was generated from 1 µg of total RNA for each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit (P/N 4363105) according to the manufacturer’s protocol.
 
Hybridization protocol Hybridization protocol Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.
Scan protocol Scan protocol Chemiluminescent Detection Kit (P/N 4339627, http://docs.appliedbiosystems.com/pebiodocs/04339627.pdf) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).
Description NA
Data processing Data processing The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.
 
Submission date Dec 16, 2006
Last update date Apr 01, 2011
Contact name Jay Woo Shin
E-mail(s) jay.shin@gsc.riken.jp
Organization name ETH Zurich
Department Institute of Pharmaceutical Sciences
Lab Michael Detmar
Street address Wolfgang-Paulistrasse 10; HCI H394
City Zurich
State/province Zurich
ZIP/Postal code 8093
Country Switzerland
 
Platform ID GPL2986
Series (2)
GSE6549 Identification of the vascular lineage-specific transcriptome
GSE6560 Vascular lineage-specific transcriptome

Data table header descriptions
ID_REF
SN Signal to Noise Ratio
Flag Quality Flag value; a 'good' Flag value is any value <5000
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE Quantiled normalized

Data table
ID_REF SN Flag VALUE UNF_VALUE
226434 2.75 0 453.9 453.9
217298 1 1 307.72 307.72
235313 1.54 0 399.06 399.06
221147 0.4 1 414.01 414.01
225648 0.17 1 316.19 316.19
201297 -0.39 1 140.82 140.82
225574 -1.21 1 227.77 227.77
227207 2.7 0 675.37 675.37
226681 1.9 0 377.05 377.05
112566 0.72 1 1601.87 1601.87
165590 0.82 1 552.9 552.9
102999 3.1 0 623.19 623.19
117084 7.08 64 878.72 878.72
213726 0.38 1 945.72 945.72
185626 6.12 0 784.98 784.98
106630 -0.67 1 591.55 591.55
147245 -1.1 1 297.88 297.88
170698 46.73 0 76078.8 76078.8
164432 38.29 0 148777.2 148777.2
171597 -0.73 1 482.11 482.11

Total number of rows: 30344

Table truncated, full table size 883 Kbytes.




Supplementary file Size Download File type/resource
GSM151635.txt.gz 208.0 Kb (ftp)(http) TXT

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