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Sample GSM2165928 Query DataSets for GSM2165928
Status Public on May 20, 2016
Title Primary Mouse_SQ1 treated_Replicate4
Sample type RNA
 
Channel 1
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 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_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 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_8
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 0.2124247
A_55_P1991598 -0.8703469
A_55_P2022211 0.22591347
A_55_P1980764 1.410977
A_55_P1964375 -0.03222572
A_51_P128876 -0.16703594
A_55_P2121042 -0.006566515
A_52_P219230 -0.86203486
A_51_P207591 -0.3670517
A_55_P2131920 -0.15885405
A_55_P2404223 0.2047668
A_55_P2101944 -0.4002962
A_52_P358860 0.18463051
A_51_P119031 0.002317324
A_51_P309854 0.35032374
A_51_P343900 0.014775129
A_51_P234359 0.15099005
A_51_P487813 -0.17360687
A_52_P613977 0.076453224
A_55_P1957209 0.19867478

Total number of rows: 39483

Table truncated, full table size 960 Kbytes.




Supplementary file Size Download File type/resource
GSM2165928_SQ17_A647_VS_CON7_A555_mo.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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