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Sample GSM2165905 Query DataSets for GSM2165905
Status Public on May 20, 2016
Title Primary Rat_SQ1 treated_Replicate1
Sample type RNA
 
Channel 1
Source name primary hepatocytes_untreated control
Organism Rattus norvegicus
Characteristics strain: Sprague Dawley
gender: male
cell type: Primary cultured Rat 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 Rattus norvegicus
Characteristics strain: Sprague Dawley
gender: male
cell type: Primary cultured Rat 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 Rt SQ1_1
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 GPL14746
Series (2)
GSE81657 Rat 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_64_P076162 0.22354174
A_64_P002176 0.029352615
A_42_P664913 -0.116142325
A_43_P13320 0.21362592
A_64_P126523 0.09076727
A_64_P038045 -0.3578403
A_43_P11804 -0.11823945
A_44_P808710 0.22762755
A_64_P142111 0.46556044
A_64_P095642 -0.2665062
A_42_P735279 -0.27161598
A_44_P902822 -0.037717424
A_42_P563843 0.2917328
A_42_P610788 1.5575485
A_44_P242429 0.3658485
A_64_P020571 -0.15225978
A_42_P518462 0.29339403
A_42_P469751 3.0101304
A_44_P209459 0.54259384
A_64_P018547 0.82380784

Total number of rows: 30421

Table truncated, full table size 721 Kbytes.




Supplementary file Size Download File type/resource
GSM2165905_CON3_VS_SQ17_rt.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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