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Sample GSM7188104 Query DataSets for GSM7188104
Status Public on Dec 01, 2023
Title GXpoly_9
Sample type RNA
 
Source name Colon mucosa of a rat fed a diet containging GXpoly, replicate 9
Organism Rattus norvegicus
Characteristics strain: Wistar
Sex: female
date: 2021-01-20
treatment: extract rich in polyphenol and glucoronoxylan
sample type: GXpoly
tissue type: mucosa of colon mid-segment
cage: 12
slide: 2
slide position: 2_2
rin: 9.3
group: 3
260/280 ratio: 2.08
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_2_2.txt
Gene expression from the colon mucosa of a female rat fed a diet containing polyphenol-and GX-rich extract (10% w/w)
PAm32
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

Data table header descriptions
ID_REF
VALUE Log2 transformed and quantile normalized values

Data table
ID_REF VALUE
1 14.52054461
2 5.619321795
3 5.497698102
4 5.695672546
5 5.497698102
6 6.22372448
7 5.944232953
8 10.18312749
9 7.20751372
10 5.73461984
11 6.358560387
12 13.65542217
13 9.065138587
14 6.497444267
15 6.358560387
16 6.30815388
17 6.645961074
18 7.054831651
19 6.174532039
20 6.143593998

Total number of rows: 62976

Table truncated, full table size 1088 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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