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Sample GSM7188085 Query DataSets for GSM7188085
Status Public on Dec 01, 2023
Title pureGX_2
Sample type RNA
Source name Colon mucosa of a rat fed a diet containging pureGX, replicate 2
Organism Rattus norvegicus
Characteristics strain: Wistar
Sex: male
date: 2021-01-18
treatment: purified glucuronoxylan
sample type: pureGX
tissue type: mucosa of colon mid-segment
cage: 1
slide: 2
slide position: 2_1
rin: 9.5
group: 1
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_1.txt
Gene expression from the colon mucosa of a male rat fed a diet containing hihgly purified GX (10% w/w)
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
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
VALUE Log2 transformed and quantile normalized values

Data table
1 13.22123948
2 5.447550567
3 5.447550567
4 5.70222308
5 5.484241336
6 6.04596205
7 5.417304134
8 10.17517603
9 7.117821381
10 5.548906576
11 5.548906576
12 13.58279188
13 9.086071635
14 5.9839424
15 6.273734699
16 5.599046214
17 6.143956123
18 6.006399028
19 5.548906576
20 5.832099155

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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