|
| Status |
Public on Jul 09, 2017 |
| Title |
MMC38 vs MMC32 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Cocoa fiber diet
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Colon
gender: Female
rat strain: Wistar
age: Six week old
dietary intervention: Cocoa fiber diet
|
| Treatment protocol |
Tissue samples were transfered into lysing matrix tubes containing an appopriate buffer and were homogenized in a FastPrep® instrument for 30 s. Lysate were centrifuged for 3 min at 12.000 g to aliminate excess tissue debris.
|
| Growth protocol |
At the end of the nutritional intervention, a 5 mm piece of the middle of the colon was collected from all animals in aseptic conditions in RNAlater® and kept at 4 ºC overnight before storing at -20 ºC for further gene expression analysis by microarray.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was isolated by the RNeasy Mini Kit following the manufacturer's recommendations and quantified with a NanoDrop spectrophoyometer and NanoDrop IVD-1000 v.3.1.2 software. The agilent 2100 Bioanalyzer with the RNA 600 LabChip kit was used to provide an RNA integrity number for each sample.
|
| Label |
Cy5
|
| Label protocol |
Two-color microarray-based LowInput QuickAmp Labeling (Agilent)
|
| |
|
| Channel 2 |
| Source name |
Inulin diet
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Colon
gender: Female
rat strain: Wistar
age: Six week old
dietary intervention: Inulin diet
|
| Treatment protocol |
Tissue samples were transfered into lysing matrix tubes containing an appopriate buffer and were homogenized in a FastPrep® instrument for 30 s. Lysate were centrifuged for 3 min at 12.000 g to aliminate excess tissue debris.
|
| Growth protocol |
At the end of the nutritional intervention, a 5 mm piece of the middle of the colon was collected from all animals in aseptic conditions in RNAlater® and kept at 4 ºC overnight before storing at -20 ºC for further gene expression analysis by microarray.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was isolated by the RNeasy Mini Kit following the manufacturer's recommendations and quantified with a NanoDrop spectrophoyometer and NanoDrop IVD-1000 v.3.1.2 software. The agilent 2100 Bioanalyzer with the RNA 600 LabChip kit was used to provide an RNA integrity number for each sample.
|
| Label |
Cy3
|
| Label protocol |
Two-color microarray-based LowInput QuickAmp Labeling (Agilent)
|
| |
|
| |
| Hybridization protocol |
Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).
|
| Scan protocol |
Scanned on an Agilent G2505C scanner
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)
|
| |
|
| Submission date |
Jul 15, 2015 |
| Last update date |
Jul 09, 2017 |
| Contact name |
Francisco Jose Pérez-Cano |
| E-mail(s) |
[email protected]
|
| Organization name |
Universitat de Barcelona
|
| Department |
Departament de Fisiologia-Farmàcia
|
| Street address |
Edifici B, 3a planta, Av. Joan XXIII s/n
|
| City |
Barcelona |
| State/province |
Catalunya |
| ZIP/Postal code |
08028 |
| Country |
Spain |
| |
|
| Platform ID |
GPL14797 |
| Series (1) |
| GSE70950 |
Cocoa polyphenols and fiber modify colonic gene expression in rats |
|
