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Sample GSM952648 Query DataSets for GSM952648
Status Public on Jun 25, 2015
Title Monolayer-cultured hepatocytes 3
Sample type RNA
 
Source name Monolayer-cultured hepatocytes extracted from rat #3
Organism Rattus norvegicus
Characteristics treatment: Monolayer-cultured
cell type: primary hepatocyte
genetic background: F344/DuCrlCrlj
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the four kinds of samples mentioned above using an RNeasy Plus Micro Kit (Qiagen GmbH, Germany) according to the manufacturer’s instructions. Quantity and quality of RNA were determined by a Nanodrop ND-1000 spectrophometer (Thermo Fisher Scientific Inc., Waltham, MA) and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), as recommended.
Label Cy3
Label protocol Total RNA was amplified and labeled with Cyanine 3 (Cy3) using an Agilent Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies, Palo Alto, CA) following the manufacturer's instructions. Briefly, 100 ng of total RNA was reverse-transcribed to double-strand cDNA by using a poly dT-T7 promoter primer. Primer, template RNA, and quality-control transcripts of known concentration and quality were first denatured at 65ºC for 10 min and incubated for two hours at 40ºC with 5X first-strand buffer, 0.1-M DTT, 10-mM dNTP mix, and AffinityScript RNase Block Mix. The AffinityScript enzyme was inactivated at 70ºC for 15 min. cDNA products were then used as templates for in vitro transcription to generate fluorescent cRNA. cDNA products were mixed with a transcription master mix in the presence of T7 RNA polymerase and Cy3 labeled-CTP and incubated at 40ºC for two hours. The labeled cRNAs were purified using Qiagen’s RNeasy mini spin columns and eluted in 30 μl of nuclease-free water. Subsequently, amplified cRNA quantity and labeled cyanine incorporation were determined using a Nanodrop ND-1000 spectrophometer and an Agilent bioanalyzer.
 
Hybridization protocol 1.65 ug of Cy3-labeled cRNA was fragmented and hybridized at 65ºto the Agilent Whole Rat Genome Microarrays 4× 014879).
Scan protocol Microarrays were scanned using an Agilent DNA microarray scanner.
Description Gene expression in monolayer-cultured hepatocytes
Data processing The microarray data were analyzed by using the GeneSpring GX 10.0.2. (Agilent Technologies)
Intensity values of each scanned feature were quantified using Agilent Feature Extraction Software version 10.5.1.1, which performs background subtractions.
 
Submission date Jun 26, 2012
Last update date Jun 25, 2015
Contact name Ryosuke Takahashi
E-mail(s) ryosuke.takahashi.jr@hitachi.com
Organization name Hitachi, Ltd.
Department Central Research Laboratory
Lab Advanced Research Department
Street address 2520 Hatoyama
City Saitama
ZIP/Postal code 3500395
Country Japan
 
Platform ID GPL7294
Series (1)
GSE38950 Comprehensive expression analysis of primary hepatocytes under four different culture conditions

Data table header descriptions
ID_REF
VALUE default normalized Agilent gProcessedSignal
detection

Data table
ID_REF VALUE detection
GE_BrightCorner -0.80381775 P
DarkCorner -0.55886745 M
A_44_P465448 0.043424606 A
A_44_P514796 -0.19149494 P
A_44_P409518 0.2792201 A
A_44_P279262 -0.48292923 A
A_44_P375042 0.55694175 P
A_44_P269499 0.16796875 P
A_44_P204808 -0.54560995 A
A_44_P438090 0.076043844 P
A_44_P330643 -0.28207088 P
A_44_P421941 -0.5480137 A
A_42_P504653 -1.9409757 P
A_44_P260580 -0.093688965 P
A_44_P445440 -0.034184456 A
A_44_P313825 -0.05532217 P
A_44_P788423 0.07640123 A
A_44_P549509 0.33860207 P
A_43_P12354 -0.71095014 P
A_43_P14989 0.07250738 P

Total number of rows: 41090

Table truncated, full table size 1049 Kbytes.




Supplementary file Size Download File type/resource
GSM952648_MONO3.txt.gz 7.5 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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