|
| Status |
Public on Mar 27, 2024 |
| Title |
4T1_Singles-CDH1_rep2 |
| Sample type |
genomic |
| |
|
| Source name |
Single cells with CDH1 overexpressed from the 4T1 cell line
|
| Organism |
Mus musculus |
| Characteristics |
subpopulation: Singles-CDH1
|
| Treatment protocol |
No treatment
|
| Growth protocol |
37 C, 5% CO2; grown in DMEM media with 10% FBS, 1% penicillin-streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were grown to 70% confluency, trypsinized and then homogenized using QIAshredder (Qiagen #79654). DNA was isolated using the QIAamp DNA Mini Kit (Qiagen #51304).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
Bisulfite conversion was performed on the DNA, and the DNA was applied to the Infinium Mouse Methylation BeadChip (Illumina, 20041558)
|
| Scan protocol |
standard Illumina scanner
|
| Data processing |
Data from each sample was first pre-processed by R package “sesame” and differentially methylated positions (DMPs) were detected by function “dmpFinder” implemented in R package “minfi”
|
| |
|
| Submission date |
Mar 22, 2024 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Adam Marcus |
| E-mail(s) |
aimarcu@emory.edu
|
| Organization name |
Emory University
|
| Street address |
1365 Clifton Rd NE, Building C, Room 4092
|
| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL31950 |
| Series (1) |
| GSE262287 |
DNA methylation profiles of 4T1 invasively-distinct subpopulations |
|
