|
| Status |
Public on Dec 01, 2023 |
| Title |
control_7 |
| Sample type |
RNA |
| |
|
| Source name |
Colon mucosa of a rat fed a control diet, replicate 7
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
Sex: female
date: 2021-01-18
treatment: cellulose
sample type: control
tissue type: mucosa of colon mid-segment
cage: 10
slide: 2
slide position: 1_2
rin: 9.4
group: 2
260/280 ratio: 2.1
|
| Treatment protocol |
The four-weeks-old female and male Wistar (RccHan: WIST) rats purchased from Envigo Netherlands (Horst, The Netherlands) were fed pelleted, modified AIN-93G diets (Envigo Teklad Diets, Madison WI, The United States) containing either 10% (w/w) of cellulose (control group), 10% of polyphenol-and GX-rich extract (GXpoly), or 10% of highly purified GX (pureGX) after 12 days of acclimatization.
|
| Growth protocol |
The animal study protocol was approved by the Finnish National Animal Experiment Board (Eläinkoelautakunta, ELLA; permit code: ESAVI/12806/2019), and the research was carried out according to ARRIVE guidelines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction, the mucosa of colon mid-segment (2cm) was collected using a microscope slide and stored in RNALater for 24 hours at +4°C, after which it was transferred to -20°C. Total RNA was extracted with TRIzol Plus RNA Purification Kit (12183555, Invitrogen) according to manufactures instructions. Samples with RIN values > 8 were used for the analysis.
|
| Label |
Cy5
|
| Label protocol |
Samples (200 ng) were amplified using the T7 RNA polymerase method. cRNAs were labelled with Cy3 or Cy5 following the manufacturer's protocol (Agilent).
|
| |
|
| Hybridization protocol |
Labeled cRNA samples were hybridised onto the Agilent 2-colour 8x60k arrays according to the manufacturer's recommendations and hybridized for 17 hours at 65°C. After hybridization, slides were washed following the manufacturer's instructions (Agilent).
|
| Scan protocol |
Slides were scanned with Agilent microarray scanner G2505C and data were extracted using the Agilent Feature Extraction software (V12.0.2.2.)
|
| Description |
US11263921_257403611527_S01_GE2_1200_Jun14_1_2.txt
Gene expression from the colon mucosa of a female rat fed a control diet (10% w/w cellulose)
PAm24
|
| Data processing |
Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and data were log2 transformed and normalized with quantile normalization. This experiment was performed as a two-colour experiment, but data were analyzed as single-channel arrays. Raw data files are available as a tar archive on the series record.
|
| |
|
| Submission date |
Apr 20, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Dario Greco |
| E-mail(s) |
dario.greco@tuni.fi
|
| Organization name |
Tampere University
|
| Department |
Faculty of Medicine and Health Technology
|
| Lab |
Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)
|
| Street address |
Arvo ylpön Katu 34
|
| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL22145 |
| Series (1) |
| GSE230139 |
Diet supplemented with polyphenol- and glucuronoxylan-rich fiber extract regulates colonic barrier function and cell proliferation in healthy rats |
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