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Sample GSM953752 Query DataSets for GSM953752
Status Public on Jun 30, 2012
Title knockout rep-2
Sample type RNA
 
Source name Mouse soleus
Organism Mus musculus
Characteristics tissue: skeletal muscle
strain: mixed background (C57Bl/6 and 129)
genotype: Yin Yang 1 (YY1) knockout
age: 6 months
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) waas purified from the IVT reaction mixture using magnetic particles. The cRNA was quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution was then removed. The chips were transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Scan protocol Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, GCS3000, and the positions and intensities of the fluorescent emissions were captured.
Description Gene expression data from knockout soleus
Data processing The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method RMA quantile normalization yes background correct yes compute present absent calls no normalization method none value to scale to clm file annotate probes yes The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method RMA quantile normalization yes background correct yes compute present absent calls no normalization method none value to scale to clm file annotate probes yes.
 
Submission date Jun 28, 2012
Last update date Jun 30, 2012
Contact name Pere Puigserver
E-mail(s) pere_puigserver@dfci.harvard.edu
Phone 617-582-7977
Organization name Dana-Farber Cancer Institute
Street address 450 Brookline Av. CLSB-11144
City Boston
ZIP/Postal code 02215
Country USA
 
Platform ID GPL8321
Series (1)
GSE39009 Expression data from mouse skeletal muscle

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
1415670_at 719.3459519
1415671_at 1446.774523
1415672_at 2184.9946
1415673_at 271.9962997
1415674_a_at 612.0471166
1415675_at 356.6727624
1415676_a_at 3824.942999
1415677_at 744.4888091
1415678_at 6593.432569
1415679_at 5376.129182
1415680_at 527.2540354
1415681_at 2107.041002
1415682_at 465.3594873
1415683_at 2207.774523
1415684_at 386.9067629
1415685_at 825.8394543
1415686_at 1162.694771
1415687_a_at 6511.917381
1415688_at 5763.695726
1415689_s_at 679.3459519

Total number of rows: 22690

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM953752_KO2.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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