NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2165912 Query DataSets for GSM2165912
Status Public on May 20, 2016
Title Primary Rat_SQ1 treated_Replicate8
Sample type RNA
 
Channel 1
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 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 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 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_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 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 0.11840188
A_64_P002176 0.2042665
A_42_P664913 -0.26639646
A_43_P13320 0.12644202
A_64_P126523 -0.28556058
A_64_P038045 0.2645295
A_43_P11804 -0.40540457
A_44_P808710 0.11852925
A_64_P142111 -0.047106285
A_64_P095642 0.19273753
A_42_P735279 -0.18999858
A_44_P902822 -0.13611603
A_42_P563843 0.28624314
A_42_P610788 1.9302034
A_44_P242429 -0.32627493
A_64_P020571 0.092607476
A_42_P518462 0.31614023
A_42_P469751 -0.26163834
A_44_P209459 0.1780472
A_64_P018547 0.7626953

Total number of rows: 30421

Table truncated, full table size 723 Kbytes.




Supplementary file Size Download File type/resource
GSM2165912_SQ1-18_VS_CON14_rt.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap