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Sample GSM2825804 Query DataSets for GSM2825804
Status Public on Oct 19, 2020
Title colon_water_2
Sample type RNA
 
Source name colon mucosa, drinking water
Organism Mus musculus
Characteristics strain: Balb/cJ
gender: female
tissue: colon mucosa
model_induction: water
compound: vehicle control
Treatment protocol Chronic colitis was induced in eight weeks old mice by cyclical administration of 4% DSS via drinking water, involving 3 cycles of DSS for 4 days interrupted by washout periods of 3 days under regular drinking water. The mice (n=5 per group) were assigned in 3 groups: 1/ Drinking water, 2/ DSS in water and filgotinib vehicle 3/ DSS in water and filgotinib. Filgotinib was given at 30 mg/kg, once a day by oral gavage.
Growth protocol Standard animal housing conditions
Extracted molecule total RNA
Extraction protocol For RNA preparation from mouse colon, mucosal samples were obtained by cutting lengthwise thirty millimeters of the most distal part of descending colon and scraping mucosa from the connective tissue. Mucosa was sampled into homogenization tubes containing 1.4 mm ceramic beads and was immediately snap frozen in liquid nitrogen. Mucosa samples were homogenized using the Precellys 24 homogenizer (Bertin Technologies™, France). Total RNA were isolated and further purified with NucleoSpin 96 RNA Tissue Core Kit (Macherey-Nagel™) according to the manufacturer’s instructions. RNA yield were determined by spectrophotometry at 260/280 nm.
Label Cy3
Label protocol Before labeling reaction, samples are diluted to 100 ng/ml. Then, Agilent Technologies’ Low Input Quick Amp Labeling Kit generates fluorescent cRNA with 100 ng of total RNA. The method first uses reverse transcriptase to synthesize the first and second strands of cDNA and then T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP. Before proceeding to the sample hybridization, labeled cRNA and dye concentrations are quantified with NanoDrop ND-1000 spectrophotometer (Thermo Scientific): - cRNA concentration (ng/μl), - Cyanine 3 concentration (pmol/μl). After labeling step, cRNA sample size ranges from 50 to 3000 nucleotides. Thus, fragmentation is required to take away secondary structures. Fragmentation step is achieved with specific buffer (Agilent Technologies) and allows obtaining cRNA length between 50 to 200 nucleotides and then optimal hybridization with Agilent 60-mer oligonucleotide microarrays. This step is incubation at 60°C for 30 minutes.
 
Hybridization protocol 600 ng of Cyanine 3-labeled amplified cRNA are hybridized at 65°C for 17 hours.
Scan protocol Scanning is performed with Agilent Technologies’ scanner using default parameters for 8x60k format (61*21.6 mm; 3 micrometer scan resolution; 20 bit TIFF; green channel)
Description Gene expression of control animals (drinking water)
Data processing Data are extracted with Feature Extraction 11.5.1.1 software (Agilent Technologies). This software reads and processes microarray image files to prepare them for analysis. Feature Extraction automatically assigns a grid template and a protocol, based on the barcode of the slide. It determines feature intensities, rejects outliers and calculates statistical confidences. Quality was assessed using the arrayQualityMetrics R/BioConductor package. A filter was set to remove probes that are not expressed above background (cut-off defined such that a probe must have a valid and above background signal in at least 40% of the samples). Background correction (using the “normexp” method with an offset of 16) and quantile normalization were applied to obtain log2 transformed and normalized expression data. Within-array replicate probes are summarized with the mean. Differential expression analysis was performed using empirical Bayes methods and generalized linear models (limma R/BioConductor package). All data is MIAME compliant
 
Submission date Oct 20, 2017
Last update date Oct 19, 2020
Contact name Maté Ongenaert
E-mail(s) mate.ongenaert@glpg.com
Phone +3215342927
Organization name Galapagos
Street address Generaal De Wittelaan L11A3
City Mechelen
ZIP/Postal code 2800
Country Belgium
 
Platform ID GPL21163
Series (1)
GSE105417 Selective inhibition of JAK1 with filgotinib reverses pathogenic processes in the DSS preclinical model for IBD

Data table header descriptions
ID_REF
VALUE Log2 quantile normalized and background corrected signal intensity

Data table
ID_REF VALUE
A_51_P399985 12.92734844
A_55_P2419483 7.775475193
A_55_P2739683 10.83934325
A_51_P211903 10.8805947
A_51_P226429 9.306935223
A_55_P2737159 14.554992
A_55_P2728466 9.307473874
A_55_P2101526 9.515053653
A_52_P1132414 7.991767639
A_66_P135936 16.75567046
A_55_P2805396 8.040508313
A_55_P2717104 6.670524065
A_55_P2909714 14.0642062
A_55_P2744310 11.50618808
A_52_P83363 6.644890582
A_55_P2091691 14.0393115
A_66_P106200 9.266345912
A_66_P137157 13.50824608
A_51_P389543 5.405631494
A_55_P2084656 17.26327196

Total number of rows: 32349

Table truncated, full table size 803 Kbytes.




Supplementary file Size Download File type/resource
GSM2825804_B07.txt.gz 12.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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