|
| Status |
Public on Mar 29, 2024 |
| Title |
secondCohort_WT_rep3 |
| Sample type |
genomic |
| |
|
| Source name |
genomic DNA from 10 days old mouse ear clips
|
| Organism |
Mus musculus |
| Characteristics |
Sex: male
tissue: ear
developmental stage: 10 days
batch: 1
|
| Treatment protocol |
Digestion was carried out overnight in a Thermocycler under the following conditions: 55C for 16 hours, 95C for 10 minutes, 4C hold (lid at 105C). After lysis, the lysate was diluted by adding 160 µl of nuclease-free water (Invitrogen, AM9938) to the same tube (180 µl final volume).
|
| Growth protocol |
Ear punch biopsies were collected at 10 days and placed in 20 µl reaction mix composed of genomic DNA lysis buffer (100 mM Tris-HCl pH 8.5, 5 mM EDTA, 0.2% SDS, 100 mM NaCl) supplemented with 20 mg proteinase K (Thermo Scientific, EO0491).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We used the DNeasy Blood & Tissue Kit (QIAGEN, 69504) for DNA extraction
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Infinium HD Assay Methylation Protocol document #15019519 v01
|
| |
|
| Hybridization protocol |
Bisulphite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged on the iScan using standard recommended Illumina scanner setting
|
| Description |
207656680002_R05C02
|
| Data processing |
GenomeStudio software v.2011.1 and SeSAMe
single_signal_supp.txt = Unmethylated and methylated signal intensities
processed_matrix.txt = Average Beta
|
| |
|
| Submission date |
Mar 28, 2024 |
| Last update date |
Mar 29, 2024 |
| Contact name |
Luca Fagnocchi |
| E-mail(s) |
luca.fagnocchi@vai.org
|
| Organization name |
VAI
|
| Street address |
333 Bostwick AVE NE
|
| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
| |
|
| Platform ID |
GPL30650 |
| Series (2) |
| GSE262711 |
Developmental priming of cancer susceptibility [DNA methylation array - d10earclips_2nd cohort] |
| GSE262713 |
Developmental priming of cancer susceptibility |
|
