|
| Status |
Public on Dec 18, 2019 |
| Title |
BrafWT_439693A03 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DNA immunoprecipitated with monoclonal antibody against 5-methylcytidine
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type mice
tissue: small intestine
type: wild type (WT)
Sex: female
age: more than 55 weeks (>55w)
chip antibody: monoclonal antibody against 5-methylcytidine
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions.
|
| Label |
Cy5
|
| Label protocol |
NimbleGen Dual-Color DNA Labeling Kits; untreated total DNA fraction was labeled with Cy3 and the methyled DNA fraction was labeled with Cy5.
|
| |
|
| Channel 2 |
| Source name |
INPUT
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: none, input DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions.
|
| Label |
Cy3
|
| Label protocol |
NimbleGen Dual-Color DNA Labeling Kits; untreated total DNA fraction was labeled with Cy3 and the methyled DNA fraction was labeled with Cy5.
|
| |
|
| |
| Hybridization protocol |
NimbleGen Hybridization protocol
|
| Scan protocol |
Arrays were scanned on NimbleGen MS 200 Microarray Scanner
|
| Data processing |
NimbleScan was used to produce .ndf, .pos, and .pair files. Pair files were sacled using Tukey-bi-weight scaling using Ringo R package. Unique PROBE_ID with COUNT=1 from .pos file were used for further analysis.
|
| |
|
| Submission date |
Dec 28, 2017 |
| Last update date |
Dec 18, 2019 |
| Contact name |
Faiza Noreen |
| E-mail(s) |
faiza.noreen@unibas.ch
|
| Organization name |
University of Basel
|
| Department |
Department of Biomedicine
|
| Street address |
Mattenstrasse 28
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL16446 |
| Series (2) |
| GSE98534 |
DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways |
| GSE108606 |
DNA methylation instability by BRAF-mediated TET silencing and lifestyle-exposure divides colon cancer pathways [BrafV637E knock-in ] |
|
