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Sample GSM400914 Query DataSets for GSM400914
Status Public on Jan 01, 2010
Title PMN_control_2_RNeasy
Sample type RNA
 
Source name polymorphonuclear leukocytes, control, patient 2, RNeasy RNA isolation
Organism Homo sapiens
Characteristics disease state: control
patient: 2
cell type: polymorphonuclear leukocytes
rna isolation method: RNeasy
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. For probe sets more highly expressed in healthy control samples, the call must be present/marginal in at least 5 of 7 samples; for probe sets more highly expressed in test samples, the call must be present/marginal in at least 2 of 3 samples. At least a 1.5-fold change and a T test p-value of less than 0.05 are required.
 
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 429.46 P 0.000662269
AFFX-BioB-M_at 597.014 P 5.16732e-05
AFFX-BioB-3_at 353 P 4.42873e-05
AFFX-BioC-5_at 300.793 P 0.000146581
AFFX-BioC-3_at 248.287 P 0.000195116
AFFX-BioDn-5_at 2676.36 P 4.42873e-05
AFFX-BioDn-3_at 5843.76 P 0.000169227
AFFX-CreX-5_at 19163.5 P 5.16732e-05
AFFX-CreX-3_at 21966.8 P 4.42873e-05
AFFX-DapX-5_at 1348.12 P 4.42873e-05
AFFX-DapX-M_at 3467.92 P 0.000258358
AFFX-DapX-3_at 4722.18 P 4.42873e-05
AFFX-LysX-5_at 244.645 P 0.000753643
AFFX-LysX-M_at 294.721 P 0.0012475
AFFX-LysX-3_at 767.212 P 4.42873e-05
AFFX-PheX-5_at 274.665 P 8.14279e-05
AFFX-PheX-M_at 522.218 P 6.02111e-05
AFFX-PheX-3_at 303.52 P 0.000146581
AFFX-ThrX-5_at 404.662 P 0.000195116
AFFX-ThrX-M_at 652.549 P 8.14279e-05

Total number of rows: 54675

Table truncated, full table size 1626 Kbytes.




Supplementary file Size Download File type/resource
GSM400914.CEL.gz 4.3 Mb (ftp)(http) CEL
GSM400914.CHP.gz 305.9 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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