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Sample GSM849852 Query DataSets for GSM849852
Status Public on Dec 01, 2012
Title Treated with RNAi against STAC3 at day 1, 24h after switching to differentiation media, 48h after treatment, R1-3
Sample type RNA
 
Source name myogenic cell line, STAC3 RNAi, day 1
Organism Mus musculus
Characteristics cell line: C2C12
cell type: myogenic cells
treatment: STAC3 RNAi
time point: day 1 (24 h after switching to differentiation media, 48 h after treatment)
Treatment protocol RNAi-treated cells were transfected with an RNAi directed against STAC3 (Invitrogen). Control cells were transfected with a high-GC content control RNAi (Invitrogen).
Growth protocol Cells at day 0 were grown in growth media, 20% FBS + DMEM. Cells at day 1 were grown in differentiation media, 2% FBS in DMEM.
Extracted molecule total RNA
Extraction protocol RNA was extracted using an RNeasy Plus RNA extraction kit (Qiagen).
Label biotin
Label protocol Samples were processed commercially at Cambridge Bioscience, UK.
 
Hybridization protocol Samples were processed commercially at Cambridge Bioscience, UK.
Scan protocol Samples were processed commercially at Cambridge Bioscience, UK.
Description R1-3
Data processing The data were filtered to remove any probes with a detection p-value above 0.01 for all the samples in the set. This removes any probes not detected at all in the set. It was done before transformation via variance stabilization and normalization in order to reduce the noise of the set before normalization. As the normalization algorithm is quantile normalization, it uses the data to fit a distribution on to it and having no expressed probe in the set would have an impact on the quality of the data. Quantile normalization was performed using the program R and the Bioconductor package Lumi (PMID 18467348).
 
Submission date Dec 15, 2011
Last update date Dec 01, 2012
Contact name Neil Bower
E-mail(s) n.bower@uq.edu.au
Organization name University of Queensland
Department Institute for Molecular Bioscience
Street address Carmody Road
City St Lucia
State/province Qld
ZIP/Postal code 4072
Country Australia
 
Platform ID GPL6887
Series (1)
GSE34474 STAC3 is required for myotube formation and myogenic differentiation in vertebrate skeletal muscle

Data table header descriptions
ID_REF
VALUE Quantile-normalized signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1250052 6.829035215 0.05448718
ILMN_2599935 7.902623416 0
ILMN_1249762 6.884172108 0.1623932
ILMN_2653194 7.964942185 0
ILMN_2445236 6.697446259 0.9198718
ILMN_1212991 7.90603792 0
ILMN_2686883 6.743443583 0.215812
ILMN_2514305 6.823703021 0.0534188
ILMN_1217583 6.781529658 0.08012821
ILMN_2728634 6.780980907 0.07264958
ILMN_3040515 6.803811658 0.0491453
ILMN_2711608 6.7341311 0.2382479
ILMN_2746142 6.660194162 0.792735
ILMN_2741249 6.974417007 0.002136752
ILMN_2736209 7.164240706 0
ILMN_2647251 6.892087045 0.3728632
ILMN_1252690 6.800084668 0.1153846
ILMN_1258931 6.661804404 0.9636752
ILMN_1255743 7.500827598 0
ILMN_2420246 6.685122165 0.9839743

Total number of rows: 24538

Table truncated, full table size 746 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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