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Sample GSM103078 Query DataSets for GSM103078
Status Public on Apr 30, 2006
Title SampleNumber: 72
Sample type RNA
 
Source name whole blood
Organism Homo sapiens
Characteristics Dx: SIRS
survival: survivor
day: 3
ptID: 10_0004
DxSurv: Sirs_Surv
PRISM: 10
steroid: yes
organism: Rickettsia
infect_site: Systemic
11kMajorGroups: Grp A
11kSubGroups: Grp A1
Treatment protocol none
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from whole blood samples using the PaxGene Blood RNA System (PreAnalytiX, Qiagen/Becton Dickson) according the manufacturer’s specifications.
Quality control steps: RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used
Label biotin
Label protocol Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to manufacturer’s instructions.
 
Hybridization protocol The protocol and conditions used during hybridization, blocking and washing: Create a hybridization cocktail for a single probe array that contains 0.05 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm
Scan protocol The image file was captured on an Affymetrix Gene Chip Scanner 3000
Description Experimental factor value: Day 1 samples = control, SIRS, or septic shock. Day 3 samples = SIRS, septic shock, or SIRS resolved
Data processing Processed with Microarray suite 5.0 (Affymetrix) to generate .CEL files that were subject to RMA normalization (Irizarry et al 2003) using GeneSpring software.
Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
GeneSpring 7.2 (Agilent technologies Inc. Palo Alto, California) was used to normalization, Clustering and filtering. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls
 
Submission date Apr 04, 2006
Last update date Feb 20, 2015
Contact name Hector R Wong
E-mail(s) hector.wong@cchmc.org
Phone 513-636-4259
Fax 513-636-4267
Organization name CIncinnati Children's Hospital Medical Center
Department Division of Critical Care Medicine
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45229-3039
Country USA
 
Platform ID GPL570
Series (1)
GSE4607 Systemic inflammatory response syndrome and septic shock

Data table header descriptions
ID_REF
VALUE
Control Value
Normalized Value

Data table
ID_REF VALUE Control Value Normalized Value
1007_s_at 0.835 1 0.835
1053_at 0.866 1 0.866
117_at 0.682 1 0.682
121_at 1.214 1 1.214
1255_g_at 1.138 1 1.138
1294_at 0.818 1 0.818
1316_at 1.095 1 1.095
1320_at 0.954 1 0.954
1405_i_at 1.614 1 1.614
1431_at 1.106 1 1.106
1438_at 1.222 1 1.222
1487_at 0.785 1 0.785
1494_f_at 1.175 1 1.175
1552256_a_at 0.754 1 0.754
1552257_a_at 0.896 1 0.896
1552258_at 1.181 1 1.181
1552261_at 0.944 1 0.944
1552263_at 1.236 1 1.236
1552264_a_at 1.621 1 1.621
1552266_at 1.034 1 1.034

Total number of rows: 54675

Table truncated, full table size 1312 Kbytes.




Supplementary file Size Download File type/resource
GSM103078.CEL.gz 4.5 Mb (ftp)(http) CEL

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