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Sample GSM400926 Query DataSets for GSM400926
Status Public on Jan 01, 2010
Title PMN_control_4_STAT60
Sample type RNA
 
Source name polymorphonuclear leukocytes, control, patient 4, STAT60 RNA isolation
Organism Homo sapiens
Characteristics disease state: control
patient: 4
cell type: polymorphonuclear leukocytes
rna isolation method: STAT60
Treatment protocol Polymorphonuclear leukocytes (PMNs) were isolated from the blood of affected patients and healthy donors.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the Qiagen RNeasy kit (or with STAT60) according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
 
Hybridization protocol cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using an Affymetrix scanner.
Description control PMNs
Data processing Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips. All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files. A pivot table with all samples was created including calls, call p-value and signal intensity for each gene. Statistical and quality filters were applied as follows. The average scaled expression must be at least 100 in at least one group.
 
Submission date May 08, 2009
Last update date Aug 28, 2018
Contact name Addie Whitney
E-mail(s) awhitney@niaid.nih.gov
Organization name NIH/NIAID/RML
Department LHBP
Lab DeLeo
Street address 903 S 4th St
City Hamilton
State/province MT
ZIP/Postal code 59840
Country USA
 
Platform ID GPL570
Series (1)
GSE16020 Patients affected with autosomal dominant monocytopenia with increased susceptibility to mycobacterial infection
Relations
Reanalyzed by GSE119087

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 809.944 P 0.000753643
AFFX-BioB-M_at 1094.97 P 4.42873e-05
AFFX-BioB-3_at 749.644 P 4.42873e-05
AFFX-BioC-5_at 796.962 P 0.000169227
AFFX-BioC-3_at 888.2 P 5.16732e-05
AFFX-BioDn-5_at 6947.92 P 4.42873e-05
AFFX-BioDn-3_at 11034.6 P 6.02111e-05
AFFX-CreX-5_at 31351.7 P 5.16732e-05
AFFX-CreX-3_at 33362.6 P 4.42873e-05
AFFX-DapX-5_at 2324.77 P 4.42873e-05
AFFX-DapX-M_at 5800.71 P 0.00010954
AFFX-DapX-3_at 6604.98 P 4.42873e-05
AFFX-LysX-5_at 355.748 P 0.000296708
AFFX-LysX-M_at 500.168 P 0.000296708
AFFX-LysX-3_at 1139.17 P 4.42873e-05
AFFX-PheX-5_at 518.17 P 4.42873e-05
AFFX-PheX-M_at 773.998 P 6.02111e-05
AFFX-PheX-3_at 571.762 P 0.000126798
AFFX-ThrX-5_at 590.312 P 9.4506e-05
AFFX-ThrX-M_at 1034.91 P 5.16732e-05

Total number of rows: 54675

Table truncated, full table size 1625 Kbytes.




Supplementary file Size Download File type/resource
GSM400926.CEL.gz 4.3 Mb (ftp)(http) CEL
GSM400926.CHP.gz 303.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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