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Sample GSM1057809 Query DataSets for GSM1057809
Status Public on Jun 21, 2013
Title Rap1 -/- liver, rep 3
Sample type RNA
 
Source name Liver, Rap1 knockout mouse -/-, 10 weeks
Organism Mus musculus
Characteristics strain/background: C57BL6/129SV (90%: 10%)
genotype/variation: Rap1 -/-
tissue: liver
age: 10 weeks
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol. The QIAGEN kit was employed for purification. RNA Integrity Numbers were in the range 6.5 to 8.5 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.
Label Cy3
Label protocol Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore.
 
Hybridization protocol Total RNA samples were analyzed on Agilent's Mouse Genome DNA microarray by following manufacturer instructions. Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.
Scan protocol Images were quantified using Agilent Feature Extraction Software (ver. 10.1.1).
Description LIVER_RAP1_KO_3
Data processing Microarray background subtraction was carried out using normexp method. Normalization was performed using quantiles. Differentially expressed genes were obtained by applying linear models with R limma package (Smyth, 2005) (Bioconductor project, http://www.bioconductor.org). To account for multiple hypotheses testing, the estimated significance level (p-value) was adjusted using Benjamini & Hochberg False Discovery Rate (FDR) correction.
 
Submission date Dec 27, 2012
Last update date Jun 21, 2013
Contact name Paula Martinez
E-mail(s) pmartinez@cnio.es
Organization name CNIO
Street address Melchor Fernandez Almagro 3
City Madrid
State/province Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL10787
Series (2)
GSE43171 RAP1 protects from obesity, diabetes and metabolic syndrome through its extra telomeric role regulating gene expression (young mouse liver)
GSE43174 RAP1 protects from obesity, diabetes and metabolic syndrome through its extra telomeric role regulating gene expression

Data table header descriptions
ID_REF
VALUE Log2 normalized signal intensity

Data table
ID_REF VALUE
A_30_P01017425 6.679359072
A_30_P01017426 6.946805725
A_30_P01017427 6.318387377
A_30_P01017428 6.934326618
A_30_P01017429 5.840561465
A_30_P01017430 6.114864669
A_30_P01017431 6.035984574
A_30_P01017432 8.446143108
A_30_P01017433 6.466446064
A_30_P01017434 6.783704176
A_30_P01017435 5.923123066
A_30_P01017436 6.159697832
A_30_P01017437 8.457602096
A_30_P01017438 5.777851056
A_30_P01017439 6.439687985
A_30_P01017440 6.599784952
A_30_P01017441 6.024949072
A_30_P01017442 7.292817647
A_30_P01017443 8.073091321
A_30_P01017444 6.046936303

Total number of rows: 55681

Table truncated, full table size 1407 Kbytes.




Supplementary file Size Download File type/resource
GSM1057809_Liv_KO_US22502553_252800514432_S01_GE1_1100_Jul11_1_3.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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