|
| Status |
Public on Mar 22, 2016 |
| Title |
control vs DEHP 28day rep 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
pancreas, DEHP 12000 ppm treated, 28day
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: CD Sprague Dawley
gender: male
age: six to seven week old
treatment: DEHP 12000 ppm
time point: 28day
|
| Treatment protocol |
Six to seven week old male CD Sprague Dawley rats (Harlan Uk) were fed RM1 powdered diet containing either Wy at 20 ppm or 50 ppm, DEHP at 12000 ppm or APFO at 300 ppm in the diet for either 1, 7, 28, or 90 days. Control animals received powdered RM1 diet ad libitum for the same duration as the test groups. Animals were sacrificed at 1, 7, 28, or 90 days by exposure to a rising concentration of carbon dioxide. Pancreas was removed and snap frozen or perfused with collagenase and centrifuged through BSA (4%) to prepare isolated acinar cells. The purity of isolated acinar cells was determined by dual immunohistochemistry of fixed smears of isolated acinar cells, using -amylase- (acinar cell specific) and cytokeratin 19 (duct cell-specific) antibodies.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pancreas (tissue) RNA and isolated acinar cell RNA was extracted with Tri reagent and purified using RNeasy Midi columns (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
1 ug pancreas (tissue) RNA or isolated acinar cell RNA was labelled with Cyanine 3/Cyanine 5 using the Agilent low input labelling kit plus according to the manufacturers instructions.
|
| |
|
| Channel 2 |
| Source name |
pancreas, control, 28day
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: CD Sprague Dawley
gender: male
age: six to seven week old
treatment: vehicle
time point: 28day
|
| Treatment protocol |
Six to seven week old male CD Sprague Dawley rats (Harlan Uk) were fed RM1 powdered diet containing either Wy at 20 ppm or 50 ppm, DEHP at 12000 ppm or APFO at 300 ppm in the diet for either 1, 7, 28, or 90 days. Control animals received powdered RM1 diet ad libitum for the same duration as the test groups. Animals were sacrificed at 1, 7, 28, or 90 days by exposure to a rising concentration of carbon dioxide. Pancreas was removed and snap frozen or perfused with collagenase and centrifuged through BSA (4%) to prepare isolated acinar cells. The purity of isolated acinar cells was determined by dual immunohistochemistry of fixed smears of isolated acinar cells, using -amylase- (acinar cell specific) and cytokeratin 19 (duct cell-specific) antibodies.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pancreas (tissue) RNA and isolated acinar cell RNA was extracted with Tri reagent and purified using RNeasy Midi columns (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
1 ug pancreas (tissue) RNA or isolated acinar cell RNA was labelled with Cyanine 3/Cyanine 5 using the Agilent low input labelling kit plus according to the manufacturers instructions.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed using Agilent wash buffers according to the Agilent two colour protocol (Agilent part No G4140-90050).
|
| Scan protocol |
Agilent FE 8.5.1.1 software, GE2 scan protocol, Agilent G2565B scanner
|
| Description |
Biological replicate 2 of 5. Pancreas tissue taken from rats exposed to Wyeth 14,643 (Wy) 50ppm, Wy 20ppm, APFO 300ppm or DEHP 12000 ppm in the diet.
|
| Data processing |
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Rosetta resolver was used to generate 'signature' lists of significantly (p<0.01) altered genes using the Resolver error model by generating an error weighted mean of the 5 replicate arrays per treatment .
|
| |
|
| Submission date |
Dec 22, 2011 |
| Last update date |
Mar 22, 2016 |
| Contact name |
Simon Plummer |
| E-mail(s) |
[email protected]
|
| Phone |
+44(0)1382542088
|
| Organization name |
Micromatrices Associates ltd
|
| Street address |
23 Wellgate Street
|
| City |
Newort on tay |
| ZIP/Postal code |
DD68HS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL890 |
| Series (1) |
| GSE34651 |
Mechanisms of Pancreatic Acinar Cell Neoplasia Associated with Gene Expression Changes caused by Dietary Exposure of Rats to Ammonium perfluorooctanoate, Wyeth 14,643 or Diethylhexyl phthalate |
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