NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM953753 Query DataSets for GSM953753
Status Public on Jun 30, 2012
Title knockout rep-3
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 639.3717696
1415671_at 1531.786767
1415672_at 2176.447478
1415673_at 268.6971117
1415674_a_at 684.5501141
1415675_at 355.4939552
1415676_a_at 4197.338963
1415677_at 763.1815462
1415678_at 6291.714073
1415679_at 5323.50632
1415680_at 476.1765896
1415681_at 2093.299067
1415682_at 421.6800286
1415683_at 2218.945405
1415684_at 416.0967895
1415685_at 791.6632953
1415686_at 1237.203095
1415687_a_at 7011.764089
1415688_at 5467.488527
1415689_s_at 618.6741379

Total number of rows: 22690

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM953753_KO3.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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