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Sample GSM104488 Query DataSets for GSM104488
Status Public on Sep 01, 2006
Title HUVEC/NmenMC58_pilD_4h_rep1_1103
Sample type RNA
 
Source name Human Umbilical Vein Endothelial Cells (HUVEC)
Organism Homo sapiens
Characteristics Tissue: endothelial cells
Biomaterial provider PromoCell Cat. no. C-12200-human umbilical vein endothelial cells; INSERM U570, Faculté de Médecine René Descartes, Paris, France, prof. Xavier Nassif - Neisseria meningitidis MC58
Treatment protocol Monolayers of HUVECs in 9 cm Petri dishes infected with Neisseria meningitidis MC58 delta pilD were washed and collected into Trizol by cell-scraper
Growth protocol Confluent monolayers of HUVECs in 9 cm Petri dishes were infected with Neisseria meningitidis MC58 delta pilD (MOI=10) and cultivated in RPMI medium, 5% CO2, humidified atmosphere, 37°C, 4 hours
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was purified on RNeasy minicolumns (Qiagen) and by NaOAc/ethanol precipitation.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
 
Hybridization protocol Following fragmentation, cRNA was hybridized for 16 hr at 45C on Affymetrix Human Genome HG-U133A GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station.
Scan protocol GeneChips were scanned using the Agilent GeneArray scanner.
Description Gene expression data from HUVEC infected with Neisseria meningitidis MC58 delta pilD, 4 hours infection
Data processing The data were analyzed with RMA and MAS 5.0 algorithms using Biocondutor 1.7 and default analysis settings.
 
Submission date Apr 10, 2006
Last update date Apr 10, 2006
Contact name Marek Basler
E-mail(s) basler@biomed.cas.cz
Phone +420 2 4106 2762
URL http://l125lsx.mbu.cas.cz/Lab125/index.html
Organization name Institute of Microbiology, Czech Academy of Sciences
Department Cell and Molecular Microbiology Division
Lab Laboratory of Molecular Biology of Bacterial Pathogens
Street address Videnska 1083
City Prague 4
ZIP/Postal code CZ-142 20
Country Czech Republic
 
Platform ID GPL96
Series (1)
GSE4646 Signaling of Neisseria meningitidis MC58 mutants to primary human umbilical vein endothelial cells (HUVEC)

Data table header descriptions
ID_REF
VALUE RMA-calculated Signal intensity
ABS_CALL indicates if the transcript was present (P), absent (A), marginal (M), based on MAS 5.0
DETECTION P-VALUE the significance level of the detection call, based on MAS 5.0
LOG2_VALUE Log2 transformed RMA-calculated Signal intensity, used for identification of significantly regulated genes

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE LOG2_VALUE
1007_s_at 282.0252693 P 0.01309178 8.139680623
1053_at 67.20545307 P 0.019303461 6.070506393
117_at 90.65716393 A 0.162935019 6.502349124
121_at 714.6121784 P 0.021866375 9.48101669
1255_g_at 25.40442398 A 0.162935019 4.667007848
1294_at 128.3583166 P 0.014936519 7.004032964
1316_at 54.23183664 P 0.009985415 5.761068125
1320_at 59.08977387 A 0.3395579 5.884836573
1405_i_at 27.09942822 A 0.810617086 4.760190507
1431_at 21.43116217 A 0.107301013 4.421638182
1438_at 97.09297032 A 0.500000024 6.601294941
1487_at 244.5513463 A 0.060419342 7.933993597
1494_f_at 156.1879942 P 0.039365362 7.287139751
1598_g_at 1325.305034 P 0.000561751 10.37210873
160020_at 355.7085139 P 0.019303461 8.474551696
1729_at 231.5137546 P 0.003066739 7.854954099
177_at 85.09251655 P 0.003584915 6.410960355
1773_at 60.29553827 A 0.541184238 5.913979345
179_at 613.4177638 P 0.035162814 9.260726136
1861_at 52.63428463 A 0.218983229 5.717930935

Total number of rows: 22283

Table truncated, full table size 1056 Kbytes.




Supplementary file Size Download File type/resource
GSM104488.CEL.gz 3.4 Mb (ftp)(http) CEL

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