GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM177142 Query DataSets for GSM177142
Status Public on Jul 01, 2007
Title HUVEC control_sample K
Sample type RNA
Source name HUVEC monolayer
Organism Homo sapiens
Characteristics human umbilical vein endothelial cells, passages 3
Biomaterial provider Clonetics
Treatment protocol HUVEC cells cultured in a 1:2 mixture of endothelial growth medium (EGM (Clonetics) and M199 medium (PAA, Cölbe, Germany) supplemented with 6.7% fetal bovine serum, gentamicin, amphotericin and Liquemin® N5000 (Roche, Grenzach-Wyhlen, Germany).
Growth protocol Twenty-four hours prior to addition of C. albicans, HUVEC cells were washed and placed in antibiotic-free medium.
Extracted molecule total RNA
Extraction protocol Total RNA (5 µg/experiment) from medium-stimulated controls or HUVEC exposed to C. albicans out of 4 independent experiments was prepared using RNeasy kits from Qiagen (Hilden, Germany) according to the manufacturer’s instructions. cDNA was prepared from 5 µg total RNA using the SuperScript Choice System kit (Invitrogen, Karlsruhe, Germany) with a T7-(dT)24 primer for first-strand synthesis.
Label biotin
Label protocol cRNA was synthesized from cDNA and biotinylated using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY).20µg of cRNA was fragmented by heating at 94°C for 35 min in fragmentation buffer (40 mmol/L Tris-acetate, pH 8.1, 100 mmol/l Potassium acetate, 30 mmol/L Magnesium acetate).
Hybridization protocol 10 µg of fragmented cRNA were together with control cRNAs and grid alignment oligonucleotides hybridized under constant rotation at 45°C over night (16h) to oligonucleotide. Arrays were washed and stained (label: SAPE; Gene Chip Washing and Staining Hybridization kit, Affymetrix) using the Gene Chip Fluidics Station 450 (Affymetrix).
Scan protocol Fluorescent signals were detected by the Affymetrix GeneChip Scanner 3000. Microarrays of this series were all scaled to a TGT value of 100.
Description untreated HUVEC control
Data processing Microarray data were analyzed using MicroArray Suite (MAS) software (Affymetrix). First, background-adjusted raw intensities accounting for non-specific binding by removing probe sets with insignificant differences between single perfect-matching (PM) and mismatching (MM) probes were created. Single raw values were calculated for each probe set from the median of PM/MM discrimination values. Fold-changes (log ratio changes) and "change p values" based on a signed rank test were determined for each experiment. Only genes with a change p≤0.05 for up-regulated or a change p≥0.95 for down-regulated genes in at least 3 of 4 experiments and mean log ratio changes (calculated as mean of log ratio changes of all experiments with significant change p values) of at least 2.5 or -2.5 were considered.
Submission date Mar 23, 2007
Last update date Mar 28, 2007
Contact name Dorothee Viemann
Phone +49-511-532 - 7823
Organization name Hannover Medical School
Department Department of Pediatric Pulmonology, Allergy and Neonatology
Street address Carl-Neuberg-Straße 1
City Hannover
State/province Deutschland
ZIP/Postal code 30625
Country Germany
Platform ID GPL96
Series (1)
GSE7355 Candida-induced expression profile in HUVEC

Data table header descriptions
VALUE signal value
ABS_CALL absent present call

Data table
AFFX-BioB-5_at 55.8524 P 0.0166701
AFFX-BioB-M_at 87.0236 P 0.000509415
AFFX-BioB-3_at 14.2349 A 0.382599
AFFX-BioC-5_at 134.842 P 0.000445901
AFFX-BioC-3_at 133.415 P 0.000972149
AFFX-BioDn-5_at 188.574 P 0.000169227
AFFX-BioDn-3_at 777.103 P 0.000662269
AFFX-CreX-5_at 1742.99 P 4.42873e-05
AFFX-CreX-3_at 2412.85 P 4.42873e-05
AFFX-DapX-5_at 11.7865 M 0.0584438
AFFX-DapX-M_at 3.85869 A 0.60308
AFFX-DapX-3_at 3.56504 A 0.52976
AFFX-LysX-5_at 7.63997 A 0.102165
AFFX-LysX-M_at 1.79101 A 0.659339
AFFX-LysX-3_at 5.71922 A 0.216524
AFFX-PheX-5_at 1.59826 A 0.891021
AFFX-PheX-M_at 0.845255 A 0.978098
AFFX-PheX-3_at 3.1055 A 0.686277
AFFX-ThrX-5_at 4.11849 A 0.51489
AFFX-ThrX-M_at 1.99926 A 0.712257

Total number of rows: 22283

Table truncated, full table size 668 Kbytes.

Supplementary file Size Download File type/resource
GSM177142.CEL.gz 3.7 Mb (ftp)(http) CEL
GSM177142.CHP.gz 6.4 Mb (ftp)(http) CHP
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap