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Sample GSM2165922 Query DataSets for GSM2165922
Status Public on May 20, 2016
Title Primary Mouse_SQ1 treated_Replicate6
Sample type RNA
 
Channel 1
Source name primary hepatocytes_untreated control
Organism Mus musculus
Characteristics strain: C57Bl/J
gender: male
cell type: Primary cultured Mouse Hepatocytes
treated with: none (untreated control)
Treatment protocol 48 hours after plating, hepatocytes were left untreated or treated with 100 µM SQ1 or 30 µM pravastatin for 48 hours.
Growth protocol Primary hepatocytes plated at density and maintained in Williams Medium E.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Qiagen lysis buffer following manufacturer's instructions
Label A647
Label protocol 500ng of total RNA was input to the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, Madison, WI)  to produce aminoallyl-aRNA according to the vendor’s protocol. Five ug of each aminoallyl-aRNA sample was labeled with Alexa 555 or Alexa 647 (Molecular probes/ Life Technologies, Foster City, CA).   
 
Channel 2
Source name primary hepatocytes_SQ1
Organism Mus musculus
Characteristics strain: C57Bl/J
gender: male
cell type: Primary cultured Mouse Hepatocytes
treated with: SQ1
Treatment protocol 48 hours after plating, hepatocytes were left untreated or treated with 100 µM SQ1 or 30 µM pravastatin for 48 hours.
Growth protocol Primary hepatocytes plated at density and maintained in Williams Medium E.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Qiagen lysis buffer following manufacturer's instructions
Label A555
Label protocol 500ng of total RNA was input to the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 (Epicentre, Madison, WI)  to produce aminoallyl-aRNA according to the vendor’s protocol. Five ug of each aminoallyl-aRNA sample was labeled with Alexa 555 or Alexa 647 (Molecular probes/ Life Technologies, Foster City, CA).   
 
 
Hybridization protocol 0.825µg of Alexa 555 labeled Aminoallyl-aRNA and 0.825µg of Alexa 647 labeled Aminoallyl-aRNA were mixed together and allowed to co-hybridize on the array for 17 hours at 65°C at 10rpm in the hybridization rotator.   After hybridization the slide was washed with Agilent GE Wash Buffers following the Agilent’s protocol.
Scan protocol Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Description Mo SQ1_2
Data processing Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.
 
Submission date May 19, 2016
Last update date May 20, 2016
Contact name Thomas Kocarek
E-mail(s) t.kocarek@wayne.edu
Phone 313-577-6580
Organization name Wayne State University
Department Institute of Environmental Health Sciences
Street address 6135 Woodward Ave
City Detroit
State/province MI
ZIP/Postal code 48202
Country USA
 
Platform ID GPL11202
Series (2)
GSE81658 Mouse Primary Cultured Hepatocytes: Control vs SQ1 or Pravastatin treatment.
GSE81659 Expression data from squalestatin 1- or pravastatin-treated primary cultured mouse and rat hepatocytes.

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (A647/A555 or A555/A647) representing treated/control

Data table
ID_REF VALUE
A_55_P1989846 0.32217973
A_55_P1991598 -0.34243426
A_55_P2022211 -0.19656856
A_55_P1980764 -0.7431365
A_55_P1964375 -0.025990468
A_51_P128876 -0.39931315
A_55_P2121042 -0.3392415
A_52_P219230 -0.9827716
A_51_P207591 -0.34159073
A_55_P2131920 -0.44828224
A_55_P2404223 0.18744284
A_55_P2101944 -0.471941
A_52_P358860 -0.07601257
A_51_P119031 -0.04869563
A_51_P309854 -0.17268656
A_51_P343900 -0.053853057
A_51_P234359 0.33352855
A_51_P487813 0.073377684
A_52_P613977 0.080653116
A_55_P1957209 -0.33255512

Total number of rows: 39483

Table truncated, full table size 964 Kbytes.




Supplementary file Size Download File type/resource
GSM2165922_CON4_A467_VS_SQ14_A555_mo.txt.gz 4.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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