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Sample GSM146737 Query DataSets for GSM146737
Status Public on Nov 12, 2007
Title Muscle HRT baseline 941
Sample type RNA
 
Source name vastus lateralis muscle, HRT user, baseline
Organism Homo sapiens
Characteristics Gender: female
Age: 53 at onset of intervention
menopausal status: early postmenopausal
Treatment protocol needle muscle biopsy, immediately frozen in liquid nitrogen after extrication from biobsy needle, stored at - 70 degC until RNA extraction
Extracted molecule total RNA
Extraction protocol Frozen muscle biopsy samples were homogenized in Trizol-reagent (Invitrogen Inc.) with aid of FastPrep FP120 -apparatus (MP Biomedicals). Manufacturer’s protocol was followed through the isolation procedure.
Label Cy3
Label protocol Illumina RNA amplification kit (Ambion Inc., #I1755) was used according to manufacturer’s instructions. Input amount: 500 ng of total RNA.
 
Hybridization protocol Employing protocols by Illumina Inc.; hybridization: 17 h at 55 degC
Scan protocol Using an Illumina BeadReader containin two lasers: 532 nm and 635 nm and performing with 0.8 microns resolution. The data was acquired by the BeadStudio Direct Hybridization V.1.5.0.34
Description This sample presents baseline sample of ID_941 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-interventionc
Data processing The raw data was acquired by the BeadStudio Direct Hybridization V.1.5.0.34 (Illumina inc) and quantile normalized with Inforsense KDE 3.1 (InforSense Inc.) software
 
Submission date Nov 22, 2006
Last update date Nov 12, 2007
Contact name Eija Pöllänen
E-mail(s) eija.pollanen@jyu.fi
Phone +358-14-2604531
Fax +358-14-2604600
Organization name University of Jyväskylä
Department Department of Health Sciences
Street address PO Box 35/Viveca
City Jyväskylä
ZIP/Postal code 40014
Country Finland
 
Platform ID GPL2700
Series (1)
GSE6348 Expression data of skeletal muscle from HRT users and non-users

Data table header descriptions
ID_REF
VALUE quantile normalized intensity value
BEAD_STDEV_A941 average standard deviation associated with bead-to-bead variability
Avg_NBEADS_A941 Average number of beads
Detection_A941 p-value characterizing the chance that the target signal was distinguishable from the negative controls

Data table
ID_REF VALUE BEAD_STDEV_A941 Avg_NBEADS_A941 Detection_A941
GI_10047089-S 11039.51563 196.5 42 1
GI_10047091-S 296.79375 11.4 26 0.97290323
GI_10047093-S 513.7875 14.8 30 0.98967742
GI_10047099-S 141.528125 7 36 0.44
GI_10047103-S 872.584375 19.5 29 0.99483871
GI_10047105-S 181.759375 6.2 31 0.81677419
GI_10047121-S 141.921875 6.9 28 0.45032258
GI_10047123-S 221.671875 11.9 34 0.91483871
GI_10047133-A 165.415625 8.5 28 0.70064516
GI_10047133-I 172.5375 6.6 41 0.75870968
GI_10092578-S 150.1 5.3 28 0.55096774
GI_10092585-S 201.884375 7.5 30 0.87096774
GI_10092596-S 257.425 9.4 37 0.95096774
GI_10092600-S 494.80625 16.6 27 0.98967742
GI_10092602-S 193.928125 7.4 32 0.85290323
GI_10092603-S 190.8875 5.5 42 0.84258065
GI_10092611-A 151.625 10 28 0.5716129
GI_10092616-S 141.81875 6.4 19 0.44774194
GI_10092618-S 2801.240625 49.5 43 1
GI_10092638-S 404.853125 13.1 23 0.98580645

Total number of rows: 24354

Table truncated, full table size 988 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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