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Sample GSM953754 Query DataSets for GSM953754
Status Public on Jun 30, 2012
Title knockout rep-4
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 591.2720415
1415671_at 1549.275685
1415672_at 2262.966287
1415673_at 268.6971117
1415674_a_at 612.2430706
1415675_at 329.7284281
1415676_a_at 3852.173953
1415677_at 832.5015828
1415678_at 6554.392734
1415679_at 4991.988809
1415680_at 515.7745234
1415681_at 2062.774523
1415682_at 495.541757
1415683_at 2123.68476
1415684_at 424.7529347
1415685_at 816.7745234
1415686_at 1374.767958
1415687_a_at 5719.488809
1415688_at 5313.616955
1415689_s_at 606.4633529

Total number of rows: 22690

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM953754_KO4.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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