|
| Status |
Public on Oct 11, 2011 |
| Title |
Choe_HMVEC - Shiga toxin rep5 |
| Sample type |
RNA |
| |
|
| Source name |
primary dermal neonatal microvascular endothelial cells, 10 fM Shiga toxin, 24 h
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
|
| Treatment protocol |
Post-confluent cells were treated with 10 fM Shiga toxin-2 (Stx2) for 24 and compared to untreated cells
|
| Growth protocol |
Primary human dermal neonatal microvascular endothelial cells (HMVEC) isolated from a single donor were maintained in EGM-2MV medium (Lonza) and grown in a humidified incubator with 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was purified by cesium chloride ultracentrifugation, as described previously (Chirgwin et al, 1979, Biochemistry)
|
| Label |
biotin
|
| Label protocol |
According to the standard protocol of Affymetrix
|
| |
|
| Hybridization protocol |
According to the standard protocol of Affymetrix
|
| Scan protocol |
According to the standard protocol of Affymetrix
|
| Description |
Gene expression data from human microvascular endothelial cells treated with Shiga toxin
|
| Data processing |
Raw signal intensities were pre-processed using 13 different computational methods. The base affy package was used to compute MAS5.0, RMA, dChip.PM, and dChip.PM-MM summary expression measures. GCRMA, PLIER, VSN, mgMOS, mmgMOS, q.FARMS, l.FARMS, and the method of Choe et al, were computed using Bioconductor packages or packages made freely available by the package developers. PDNN summary expression measures were determined using PerfectMatch v2.3. All pre-processing methods were used in their default implementations. Probe sets were then filtered to remove those called 'absent' by the affy package, and then submitted to Cyber-T for statistical analysis.
|
| |
|
| Submission date |
Oct 10, 2011 |
| Last update date |
Oct 11, 2011 |
| Contact name |
Philip Marsden |
| E-mail(s) |
p.marsden@utoronto.ca
|
| Organization name |
University of Toronto
|
| Department |
Faculty of Medicine
|
| Lab |
Marsden
|
| Street address |
Li Ka Shing Knowledge Institute, St. Michael's Hospital 209 Vicotria St, rm 526
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
m5b1c6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE32710 |
Effects of E. coli Shiga toxin on the gene expression profile of human microvascular endothelial cells |
|
| Relations |
| Reanalysis of |
GSM812780 |
