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Sample GSM104490 Query DataSets for GSM104490
Status Public on Sep 01, 2006
Title HUVEC/NmenMC58_pilD_4h_rep3_1114
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
Phone +420 2 4106 2762
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
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
1007_s_at 308.0774197 P 0.021866375 8.267149135
1053_at 70.62502055 P 0.027859596 6.142107477
117_at 96.24231761 A 0.302547472 6.588599479
121_at 761.2466607 P 0.024710915 9.572220184
1255_g_at 23.4433588 A 0.3395579 4.551107379
1294_at 139.66777 P 0.024710915 7.12585533
1316_at 58.87055061 P 0.005642809 5.879474216
1320_at 73.65031319 A 0.107301013 6.202619755
1405_i_at 27.31562577 A 0.965864592 4.771654569
1431_at 21.45807664 M 0.043967773 4.423448863
1438_at 106.5881198 A 0.602006318 6.735902836
1487_at 301.6937311 P 0.027859596 8.236940909
1494_f_at 184.5149973 P 0.035162814 7.527594272
1598_g_at 1749.892972 P 0.000561751 10.77305097
160020_at 713.7695914 P 0.004180367 9.47931463
1729_at 307.4194223 P 0.004180367 8.264064505
177_at 74.28115208 P 0.01309178 6.214924286
1773_at 70.3010778 A 0.320830091 6.135474903
179_at 852.4040416 A 0.081336714 9.735393623
1861_at 116.0177206 P 0.009985415 6.85820137

Total number of rows: 22283

Table truncated, full table size 1056 Kbytes.

Supplementary file Size Download File type/resource
GSM104490.CEL.gz 3.4 Mb (ftp)(http) CEL

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