NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM856971 Query DataSets for GSM856971
Status Public on May 30, 2012
Title CO-N_t1 vs. t12
Sample type RNA
 
Channel 1
Source name CO-N-t1-Fl
Organism Homo sapiens
Characteristics tissue: whole blood
time point: after one week (t1) of supplementation
race: Caucasian
gender: male
age: between 29 and 51 years
condition: normolipidemic (TC < 200 mg/dl; LDL > 130 mg/dl; TG < 150 mg /dl)
supplementation: corn oil capsules (3.05 g linoleic acid per day)
Treatment protocol Venous blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX, Hombrechtikon, Switzerland) at baseline (t0), 4 hours (t4h) after the first intake of the study products, after one week (t1), and after twelve weeks (t12) of supplementation. The collected whole blood samples were incubated for 24 hours in the PAXgene Blood RNA Tubes at room temperature. The patients gave informed consent.
Extracted molecule total RNA
Extraction protocol Total RNA from whole blood was isolated using the PAXgene Blood RNA Kit (Qiagen, Hilden, Germany) according to the manufacturer's recommended procedures. Afterwards, total RNA was purified with the Globin Clear Kit (Ambion, Applied Biosystems, Darmstadt, Germany) according to the manufacturer's instructions. Equal amounts of purified RNA samples from each member of the respective group were pooled together. This was done for all different time points (t0, t4h, t1 and t12). Therefore, four pool-samples were generated by this process for each group, which results in a total of sixteen pool-samples for the microarray experiments. This approach was chosen to reduce biological inter-individual variability, which is frequent due to the variations in relative proportions of specific blood cell subsets, gender, age, and disease state.
Label fluorescien
Label protocol During reverse transcription, 6 µg of purified total RNA was converted into fluorescein (Fl) and Biotin (B) labeled cDNA and hybridized simultaneously in one experiment to the same array. After hybridisation, FL- and B-labeled cDNAs were sequentially detected with a series of conjugate reporter molecules according to the TSA process, ultimately with Tyramide-Cy3 and Tyramide-Cy5, respectively.
 
Channel 2
Source name CO-N-t12-B
Organism Homo sapiens
Characteristics tissue: whole blood
time point: after twelve weeks (t12) of supplementation
race: Caucasian
gender: male
age: between 29 and 51 years
condition: normolipidemic (TC < 200 mg/dl; LDL > 130 mg/dl; TG < 150 mg /dl)
supplementation: corn oil capsules (3.05 g linoleic acid per day)
Treatment protocol Venous blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX, Hombrechtikon, Switzerland) at baseline (t0), 4 hours (t4h) after the first intake of the study products, after one week (t1), and after twelve weeks (t12) of supplementation. The collected whole blood samples were incubated for 24 hours in the PAXgene Blood RNA Tubes at room temperature. The patients gave informed consent.
Extracted molecule total RNA
Extraction protocol Total RNA from whole blood was isolated using the PAXgene Blood RNA Kit (Qiagen, Hilden, Germany) according to the manufacturer's recommended procedures. Afterwards, total RNA was purified with the Globin Clear Kit (Ambion, Applied Biosystems, Darmstadt, Germany) according to the manufacturer's instructions. Equal amounts of purified RNA samples from each member of the respective group were pooled together. This was done for all different time points (t0, t4h, t1 and t12). Therefore, four pool-samples were generated by this process for each group, which results in a total of sixteen pool-samples for the microarray experiments. This approach was chosen to reduce biological inter-individual variability, which is frequent due to the variations in relative proportions of specific blood cell subsets, gender, age, and disease state.
Label biotin
Label protocol During reverse transcription, 6 µg of purified total RNA was converted into fluorescein (Fl) and Biotin (B) labeled cDNA and hybridized simultaneously in one experiment to the same array. After hybridisation, FL- and B-labeled cDNAs were sequentially detected with a series of conjugate reporter molecules according to the TSA process, ultimately with Tyramide-Cy3 and Tyramide-Cy5, respectively.
 
 
Hybridization protocol Slides were incubated at 42°C for 120 min in the following preheated (42°C) solution: 5xSSPE, SDS 0.1%, BSA 1%. Slides were washed for 2 minutes in deionized water followed by a centrifugation for drying. Equal amounts of biotin-labeled cDNA and fluorescein-labeled cDNA were hybridized simultaneously in one experiment to the human whole genome OneArray™ Microarray (Phalanx Biotech Group; Belmont, CA, USA). Hybridizations were carried out overnight at 42 °C in hybridization chambers (Eppendorf AG, Hamburg, Germany). After hybridization of the samples on the microarray slides overnight, slides were washed for 5 minutes with 2xSSCP, 5 minutes with 1xSSCP and 5 minutes with 0,5xSSCP at room temperature.
Scan protocol The hybridized chips were scanned at least six times with an Axon 4000 B™ scanner at different settings, both changing the PMT and the laser power settings. Expression levels were quantified using GenePix Pro 6.0™ image analysis software (Axon Instruments, CA, USA). Artifact-associated spots were eliminated by both visual and software guided flags.
Description The human OneArray™ DNA microarray is made of sense-strand 60-mer polynucleotide probes spotted onto a proprietary chemical layer-coated microarray glass slide. Each probe is spotted onto the array using a non-contact spotting technology. Each microarray contains 30,968 human genome probes (Phalanx Biotech Group, Palo Alto, CA 94304-1124, USA).
Data processing A ratio-based normalization method was carried out. A locally weighted linear regression (Lowess) was employed as a normalization method to account for intensity-dependent effects. The mean of the data for differently labelled targets for each gene on respectively two microarrays was taken. A standard two-state pooled-variance t-test (5% probability of error) was applied to detect differentially expressed genes. VALUE is the normalized Log (base 2) ratio of the median of Channel 1 to Channel 2.

The multiple gpr files per Sample represent the multiple scans using different settings.
 
Submission date Jan 05, 2012
Last update date May 30, 2012
Contact name Simone Schmidt
E-mail(s) Schmidt@nutrition.uni-hannover.de
Organization name Leibniz University of Hannover
Department Institute of Food Science and Human Nutrition
Street address Am kleinen Felde 30
City Hannover
ZIP/Postal code 30167
Country Germany
 
Platform ID GPL6254
Series (1)
GSE34898 Whole genome gene expression profiles of normo- and dyslipidemic men after fish oil supplementation

Data table header descriptions
ID_REF
VALUE Normalized signal intensity (log2 (ch1/ch2))
F635 Median Median feature pixel intensity at 635 nm
B635 Mean feature pixel intensity at 635 nm
F532 Median Median feature pixel intensity at 532 nm
B532 Mean feature pixel intensity at 532 nm

Data table
ID_REF VALUE F635 Median B635 F532 Median B532
PH_hs_0000002 2.2133 7762 342 2734 1134
PH_hs_0000003 -2.6911 469 266 2767 1456
PH_hs_0000004 -1.0177 356 275 1447 1283
PH_hs_0000005 0 0 0 0
PH_hs_0000006 -0.28284 2736 349 4091 1187
PH_hs_0000007 -4.0837 327 282 2043 1280
PH_hs_0000008 0 0 0 0
PH_hs_0000009 -1.0541 565 251 1846 1194
PH_hs_0000010 -3.5279 423 322 2686 1521
PH_hs_0000011 -4.8218 313 274 2326 1223
PH_hs_0000012 1.2347 11314 258 6109 1411
PH_hs_0000013 1.6506 2236 258 1747 1117
PH_hs_0000014 1.5804 5299 278 2806 1127
PH_hs_0000015 0 0 0 0
PH_hs_0000016 -7.089 343 336 2094 1141
PH_hs_0000017 0 0 0 0
PH_hs_0000018 -5.0386 344 299 2655 1176
PH_hs_0000019 -4.2346 371 285 2832 1213
PH_hs_0000020 -1.2889 657 251 2165 1173
PH_hs_0000021 1.0278 1124 337 1575 1189

Total number of rows: 30968

Table truncated, full table size 1034 Kbytes.




Supplementary file Size Download File type/resource
GSM856971_B3_650_900_00100.gpr.gz 3.5 Mb (ftp)(http) GPR
GSM856971_B3_650_900_0033.gpr.gz 3.3 Mb (ftp)(http) GPR
GSM856971_B3_750_00100.gpr.gz 3.6 Mb (ftp)(http) GPR
GSM856971_B3_750_0033.gpr.gz 3.4 Mb (ftp)(http) GPR
GSM856971_B3_750_1000_00100.gpr.gz 3.7 Mb (ftp)(http) GPR
GSM856971_B3_750_1000_0033.gpr.gz 3.5 Mb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap