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Sample GSM874532 Query DataSets for GSM874532
Status Public on Feb 04, 2013
Title 101_before PCB_rep1
Sample type RNA
 
Source name basal state before placebo (PCB) diet
Organism Homo sapiens
Characteristics diet group: PCB
tissue: skeletal muscle
sample_id: 101A
Extracted molecule total RNA
Extraction protocol RNA was prepared using the mirVanaTM miRNA Isolation Kit (Applied Biosystems) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 µg RNA using the One-Color Low Input Quick Amp labeling (Agilent) according to the manufacturer's instructions, followed by purification with Absolutely RNA Nanoprep kit (Stratagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 2x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.
Description Gene Expression in basal state before PCB diet
Data processing The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters to obtain background subtracted median normalized Signal intensities.
 
Submission date Feb 13, 2012
Last update date Feb 04, 2013
Contact name emmanuelle meugnier
E-mail(s) meugnier@univ-lyon1.fr
Organization name INSERMU1060/INRA1397
Lab CarMeN
Street address Cens Eli Bat 2 D- Hopital Lyon Sud
City Pierre Bénite
ZIP/Postal code 69495
Country France
 
Platform ID GPL13497
Series (1)
GSE35764 Polyphenols protection against fructose overload

Data table header descriptions
ID_REF
VALUE log2 Median-normalized signal intensities

Data table
ID_REF VALUE
GE_BrightCorner 7.778845
DarkCorner -7.8798447
A_23_P146146 -7.8811765
A_23_P42935 -2.0213542
A_23_P117082 2.5743618
A_23_P2683 -0.31373692
A_24_P358131 -4.9139376
A_33_P3367647 -5.8223734
A_23_P157316 -3.1844735
A_32_P14850 7.0216007
A_23_P158596 -2.2826796
A_23_P350107 -0.36627865
A_23_P388190 -0.9702463
A_23_P106544 2.6882076
A_33_P3219745 -7.8859234
A_32_P85539 0.80965805
A_23_P94998 -1.544446
A_33_P3235677 -4.1087217
A_23_P417014 -7.888499
A_23_P103905 1.7664833

Total number of rows: 34183

Table truncated, full table size 793 Kbytes.




Supplementary file Size Download File type/resource
GSM874532_US45103047_252665213101_S01_GE1_107_Sep09_1_1.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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