|
| Status |
Public on Jun 30, 2009 |
| Title |
CAPE01 Male Fischer 344 12 hours after CAPE administration, replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from CAPE-treated Male Fischer 344 rat liver labeled with Cyanine-5.
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain: Fischer-344
Gender: Male
Weight: 180-200 g
Treatment: CAPE administration and sacrificed 12 h later.
Tissue: liver
Other: normal liver histology
|
| Biomaterial provider |
UPEAL CINVESTAV-IPN, Mexico City, Mexico.
|
| Treatment protocol |
20 mg/kg of CAPE and sacrificed 12 h later.
|
| Growth protocol |
Animals had free access to food (PMI Feeds Inc., Laboratories Diet) and water at all times; each rat consumed approximately 12-15 g of food and 10-15 ml of water per day. After treatment, the animals were transferred to the holding room and kept under controlled conditions of 12 h light/12 h dark, 50% relative humidity, and 21 o C. Animal care followed institutional guidelines for the use of laboratory animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sacrifice by exsanguination under ether anesthesia. Liver was excised, washed in physiological saline solution, immersed in RNalater and stored at -80ºC. Isolation of total RNA from liver samples following the instructions for Quagen Rneasy mini kit. Quality and quantity were determined by capilary electrophoresis (RNA 6000 nano assay, Agilent)
|
| Label |
Cy5
|
| Label protocol |
Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy5-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 550nm.
|
| |
|
| Channel 2 |
| Source name |
Total RNA from normal liver labeled with Cyanine-3.
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain: Fischer-344
Gender: Male
Weight: 180-200 g
Treatment: None
Tissue: liver
Other: normal liver
|
| Biomaterial provider |
UPEAL CINVESTAV-IPN, Mexico City, Mexico.
|
| Treatment protocol |
none
|
| Growth protocol |
Animals had free access to food (PMI Feeds Inc., Laboratories Diet) and water at all times; each rat consumed approximately 12-15 g of food and 10-15 ml of water per day. After treatment, the animals were transferred to the holding room and kept under controlled conditions of 12 h light/12 h dark, 50% relative humidity, and 21 o C. Animal care followed institutional guidelines for the use of laboratory animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sacrifice by exsanguination under ether anesthesia. Liver was excised, washed in physiological saline solution, immersed in RNalater and stored at -80ºC. Isolation of total RNA from liver samples following the instructions for Quagen Rneasy mini kit. Quality and quantity were determined by capilary electrophoresis (RNA 6000 nano assay, Agilent)
|
| Label |
Cy3
|
| Label protocol |
Reverse transcription of 5µg total RNA with ChipShotTM reverse transcriptase from Promega. Using Cy3-dCTP from Amersham Biosciences. The reverse transcription was made following the ChipShotTM labeling System instructions (Promega). cDNA purification was made by Promega ChipShotTM labeling Clean-up System, dye incorporation was verified by measuring the absorbance at 260, 650nm.
|
| |
|
| |
| Hybridization protocol |
8h at 42ºC in the automatic hybridization machine discovery from Ventana. After hybridization, slides were washed twice in Ribowash buffer for 5 minutes with agitation and then once with 0.1xSSC buffer.
|
| Scan protocol |
Scanning with Genepix 400A microarray scanner (Axon instruments). Image analysis was made by Genepix Pro V6 software, each spot was evaluated and selectioned to be analysed by Bioplot software.
|
| Description |
CAPE is anticarcinogenic compound from propolis bee hives.
|
| Data processing |
Background substraction with lowess allowed value 10, log transformation and LOWESS normatilization.
|
| |
|
| Submission date |
Jul 08, 2008 |
| Last update date |
Jul 09, 2008 |
| Contact name |
Adriana Marquez-Quiñones |
| E-mail(s) |
addy_mq@yahoo.com
|
| Organization name |
CINVESTAV
|
| Department |
Cell Biology
|
| Lab |
50 Experimental Carcinogenesis
|
| Street address |
AV. Instituto Politecnico Nacional No. 2508
|
| City |
Mexico |
| State/province |
DF |
| ZIP/Postal code |
07360 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL4979 |
| Series (1) |
| GSE12030 |
Gene expression profiling of hepatocarcinogenesis initiation in Fischer-344 rats. |
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