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Sample GSM756600 Query DataSets for GSM756600
Status Public on Sep 21, 2011
Title Patient 11 Preshift
Sample type RNA
 
Source name Coke-oven worker
Organism Homo sapiens
Characteristics age: 26
time-point: Preshift
work-place: Sideoven
smoking: Yes
1oph: 0.31933517474102
Extracted molecule total RNA
Extraction protocol One-half µg RNA of each sample was amplified by Illumina TotalPrep RNA Amplification Kit according to the manufacturer’s instructions (Ambion, Austin, TX).
Label Cy3
Label protocol After non-specific binding targets were washed, the hybridization arrays were conjugated with fluorescent detector of Strepavidin-Cy3.
 
Hybridization protocol Then, 10 µg of fragmented biotin-labeled cRNA was hybridized on Phalanx Human OneArray™ by Phalanx hybridization buffer at 50oC in oven for 14-16 hrs using the bubble-mixing method.
Scan protocol Finally, arrays were dried by centrifugation and scanned by DNA Microarray Scanner (Agilent Technologies, Santa Clara, US). Images from the scanned arrays were quantified using GenePix® Pro 4.0 (Molecular Devices, Sunnyvale, CA).
Description sample 106
Data processing Spots in each array with foreground median intensity of wavelength 532 nm greater than or equal to that of background median intensity plus 3 folds standard deviation of wavelength 532 nm were considered as the “Present” flag and included for the further analysis. In order to evaluate the quality of each array in the entire array experiment, three evaluation steps were performed: basic, reproducible, and diagram. In basic step, three parameters, including percentage of “Present” spots among all spots, the average intensity of “Present” spots, and coefficient of variation of intensity for control spots in the entire arrays were all considered. If any two parameters in one array were located outside the 1.5-folds interquartile range (25th-75th) of same parameters for all arrays, that array was excluded. The remaining arrays were then evaluated in reproducible steps which the repeated arrays of the same sample would pass, when their Pearson’s correlation coefficient was larger than 0.95 and “2-fold percentage” was less than 15% (sFig. 4). The “2-fold percentage” was the percentage of probes among all probes in which the ratio of the same probe between two arrays exceeded 2-fold. In the final diagram step, the density plot of repeated arrays was used to examine the intensity profile of each array. An array would pass if the profile was similar to the rest of arrays in the same phenotype groups. When the arrays passed all three steps, the raw intensity of spots were log-2 transformed for subsequent analysis. To adjust the systematic variation of experiments and dye effects, global Lowess normalizations were performed within repeated arrays of the same sample and between the samples. Spot was included for further analysis when it was “Present” in at least one of the qualified arrays.
 
Submission date Jul 08, 2011
Last update date Sep 21, 2011
Contact name Tzu Chi Lee
E-mail(s) charles@kmu.edu.tw
Organization name Kaohsiung Medical University
Department Department of Public Health
Street address Shihcyuan 1st Rd.
City Kaohsiung
ZIP/Postal code 80708
Country Taiwan
 
Platform ID GPL6254
Series (1)
GSE30504 Whole Genome Expression in Peripheral-Blood Samples of Workers Professionally Exposed to Polycyclic Aromatic Hydrocarbons

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
PH_hs_0000002 5.261198997
PH_hs_0000003 5.381803036
PH_hs_0000004 6.463195324
PH_hs_0000005 4.901622772
PH_hs_0000006 6.120900631
PH_hs_0000007 5.324286461
PH_hs_0000008 11.63330936
PH_hs_0000009 5.684997082
PH_hs_0000010 7.290326595
PH_hs_0000011 5.207121372
PH_hs_0000012 10.24818707
PH_hs_0000013 8.14991188
PH_hs_0000014 6.806476116
PH_hs_0000015 5.650200367
PH_hs_0000016 5.165075302
PH_hs_0000017 4.487205029
PH_hs_0000018 5.995136738
PH_hs_0000019 7.368039131
PH_hs_0000020 5.194979668
PH_hs_0000021 7.37653923

Total number of rows: 20435

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM756600_H0606026397.gpr.gz 2.5 Mb (ftp)(http) GPR
GSM756600_H0606026404.gpr.gz 2.5 Mb (ftp)(http) GPR
Processed data included within Sample table

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