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Sample GSM228444 Query DataSets for GSM228444
Status Public on Dec 01, 2007
Title gp91phox-/- AM 0hr_control, biological rep1
Sample type RNA
 
Source name Alveolar Macrophage (AM)
Organism Mus musculus
Characteristics AM collected from gp91phox-/-, at 0 hours (no exposure to Aspergillus fumigatus conidia)
Treatment protocol Sample AM collected at t=0
Extracted molecule total RNA
Extraction protocol RNeasy RNA extraction kit (Quiagen) was performed on AM harvested fresh according to the manufacturer's instructions from mouse lungs.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard two-cycle Affymetrix protocol from 100 nanograms total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr_at 45C on GeneChip Mouse GeneChip 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GCOS Scanner 3000.
Description Gene expression timecourse from AM following in vivo exposure to A. fumigatus conidia.
Data processing Data was analyzed with Agilent Genespring GX v. 7.3.1 using Affymetrix GCOS generated flag data from scaled CHP files, and RMA-normalized CEL files.
 
Submission date Sep 10, 2007
Last update date Aug 14, 2011
Contact name Kate McInnerney
E-mail(s) kmcinnerney@montana.edu
Phone 406-994-5666
Fax 406-994-4926
URL http://cores.montana.edu
Organization name Montana State University
Department Microbiology
Lab Functional Genomics Facility
Street address 109 Lewis Hall
City Bozeman
State/province MT
ZIP/Postal code 59717
Country USA
 
Platform ID GPL8321
Series (1)
GSE8997 XX hour expression data of AM from C57Bl/6 or gp91phox-/- mice following exposure to conidia or polystyrene beads

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 242.769 P 0.000753643
AFFX-BioB-M_at 388.765 P 4.42873e-05
AFFX-BioB-3_at 239.711 P 6.02111e-05
AFFX-BioC-5_at 797.615 P 6.02111e-05
AFFX-BioC-3_at 899.385 P 4.42873e-05
AFFX-BioDn-5_at 1964.34 P 4.42873e-05
AFFX-BioDn-3_at 2984 P 4.42873e-05
AFFX-CreX-5_at 8238.49 P 4.42873e-05
AFFX-CreX-3_at 8837.06 P 4.42873e-05
AFFX-DapX-5_at 111.765 P 8.14279e-05
AFFX-DapX-M_at 1303.85 P 5.16732e-05
AFFX-DapX-3_at 2513.06 P 4.42873e-05
AFFX-LysX-5_at 44.1026 P 0.000509415
AFFX-LysX-M_at 214.406 P 7.00668e-05
AFFX-LysX-3_at 412.091 P 9.4506e-05
AFFX-PheX-5_at 85.7823 P 0.000195116
AFFX-PheX-M_at 264.461 P 4.42873e-05
AFFX-PheX-3_at 413.859 P 4.42873e-05
AFFX-ThrX-5_at 73.3669 P 0.00401721
AFFX-ThrX-M_at 273.393 P 7.00668e-05

Total number of rows: 22690

Table truncated, full table size 706 Kbytes.




Supplementary file Size Download File type/resource
GSM228444.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM228444.CHP.gz 122.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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