|
| Status |
Public on Sep 21, 2022 |
| Title |
Dnmt3aVillin672, 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 {delta}IEC
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 |
Dnmt3aVillin672
|
| 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 |
|
