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Sample GSM211672 Query DataSets for GSM211672
Status Public on Oct 01, 2007
Title D39delta-cps, biological rep3
Sample type RNA
 
Source name Detroit 562 infec. w. D39delta-cps
Organism Homo sapiens
Characteristics Pharyngeal epithelial cells
Treatment protocol After a 2h incubation period, nonadherent bacteria were removed by three washes with PBS
Growth protocol Monolayers of Detroit 562 cells in tissue culture dishes (60 mm) were washed twice with PBS, after which bacteria were added at a multiplicity of infection of 20:1 (bacteria:cells). Uninfected control cells were incubated with RPMI 1640 medium with 1% FCS only (mock-infected).
Extracted molecule total RNA
Extraction protocol After washing, Detroit 562 cells were lysed directly in the tissue culture dish by addition of RLT buffer (Qiagen Benelux B.V.), collected with a rubber policeman, and transferred to a microcentrifuge tube. Subsequently, total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 20 ug of cRNA were hybridized for 16 hr on Affymetrix Human Genome U133 Plus 2.0 GeneChip s. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using an Affymetrix GeneChip Scanner.
Description Gene expression data from pharyngeal epithelial cells
Data processing The data were analyzed with GeneSpring 7.3. Normalization was performed by the standard RMA-algorithm. Subsequent ratios were calculated between median folds per condition and the median fold for the appropriate control condition
 
Submission date Jul 19, 2007
Last update date Aug 28, 2018
Contact name Hester Bootsma
E-mail(s) [email protected]
Phone +31-243666332
Organization name Radboud University Medical Centre
Department Pediatrics
Lab Laboratory of Pediatric Infectious Diseases
Street address Kapittelweg 29
City Nijmegen
ZIP/Postal code 6525 EN
Country Netherlands
 
Platform ID GPL570
Series (1)
GSE8527 Analysis of the in vitro transcriptional response of human pharyngeal epithelial cells to adherent pneumococci
Relations
Reanalyzed by GSE64985
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE normalized signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 197.2 P 0.001796
AFFX-BioB-M_at 221.8 P 0.000446
AFFX-BioB-3_at 104.3 P 0.021902
AFFX-BioC-5_at 323.9 P 0.00006
AFFX-BioC-3_at 304.9 P 0.000052
AFFX-BioDn-5_at 1083 P 0.000044
AFFX-BioDn-3_at 2673.5 P 0.00007
AFFX-CreX-5_at 4630.5 P 0.000052
AFFX-CreX-3_at 6293.5 P 0.000044
AFFX-DapX-5_at 225.4 P 0.00011
AFFX-DapX-M_at 428.8 P 0.000972
AFFX-DapX-3_at 638.7 P 0.000095
AFFX-LysX-5_at 36.8 A 0.185131
AFFX-LysX-M_at 56.1 A 0.067678
AFFX-LysX-3_at 73.7 P 0.000169
AFFX-PheX-5_at 54.3 P 0.00762
AFFX-PheX-M_at 60.4 A 0.083592
AFFX-PheX-3_at 84.9 P 0.018281
AFFX-ThrX-5_at 91.4 P 0.000857
AFFX-ThrX-M_at 103.7 P 0.000258

Total number of rows: 54675

Table truncated, full table size 1414 Kbytes.




Supplementary file Size Download File type/resource
GSM211672.CEL.gz 5.5 Mb (ftp)(http) CEL
GSM211672.EXP.gz 356 b (ftp)(http) EXP
Processed data included within Sample table

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