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Sample GSM6436766 Query DataSets for GSM6436766
Status Public on Sep 21, 2022
Title Dnmt3aVillin657, DNA
Sample type genomic
 
Source name epithelial crypts
Organism Mus musculus
Characteristics disease state: DSS-induced ulcerative colitis model
cell type: epithelial crypts
genotype: Dnmt3a fl/fl
treatment: Recovery for 7 days after 5 day DSS treatment
Treatment protocol For DSS experiments, mice were treated with 2%DSS for 5 days followed by 7 days of normal drinking water.
Growth protocol Caco-2 cells were maintained in MEM medium containing 20% (vol/vol) FCS at 37 °C with 5 % CO2.
Extracted molecule genomic DNA
Extraction protocol DNA was isolated from Caco-2 cells, purified IECs and intestinal crypts using DNeasy Blood and Tissue Kit (Qiagen) according to manufacturer´s instructions.
Label Cy3, Cy5
Label protocol Standard Illumina protocol
 
Hybridization protocol For Caco-2 cells, bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Infinium Methylation EPIC Beadchip using standard Illumina protocol: For mice tissue, bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation-12v1-0 Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using iScan using standard recommended Illumina scanner setting
Description Dnmt3aVillin657
Data processing DNA methylation data was analyzed using the Bioconductor package RnBeads (version 1.12.1) with human reference genome version hg19.
The signal intensity values were normalized using the dasen method. The human and mouse data were normalized separately.
 
Submission date Aug 08, 2022
Last update date Sep 21, 2022
Contact name Neha Mishra
E-mail(s) n.mishra@ikmb.uni-kiel.de
Organization name Institute of Clinical Molecular Biology
Lab Cell biology Lab
Street address Rosalind-Franklin-Str. 12
City Kiel
ZIP/Postal code 24105
Country Germany
 
Platform ID GPL31950
Series (2)
GSE210721 DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon [Array]
GSE210763 DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon

Data table header descriptions
ID_REF
VALUE normalized signal
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
cg36602902_BC11 0.640170935 0
cg36603287_TC21 0.443900379 0
cg36603393_BC21 0.740162199 0
cg36603791_TC21 0.662129547 0
cg36603848_TC21 0.862476515 0
cg36604001_TC21 0.676873346 0
cg36604489_TC21 0.540763902 0
cg36604958_TC21 0.789664771 0
cg36605010_TC21 0.752403511 0
cg36605172_BC21 0.788065854 0
cg36605223_TC21 0.799201938 0
cg36605802_TC21 0.713380983 0
cg36605876_BC11 0.04289124 0
cg36605883_TC21 0.092116191 0
cg36605884_BC21 0.077157067 0
cg36605929_TC21 0.057582917 0
cg36608050_BC21 0.303425074 0
cg36608613_TC11 0.849847255 0
cg36608851_TC11 0.098231074 0
cg36608937_TC11 0.301799838 0

Total number of rows: 207208

Table truncated, full table size 6012 Kbytes.




Supplementary file Size Download File type/resource
GSM6436766_206011040039_R03C01_Grn.idat.gz 2.6 Mb (ftp)(http) IDAT
GSM6436766_206011040039_R03C01_Red.idat.gz 2.6 Mb (ftp)(http) IDAT
Processed data included within Sample table

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