|
| Status |
Public on Jan 20, 2017 |
| Title |
SUM229neg_DMSO_24h |
| Sample type |
genomic |
| |
|
| Source name |
EpCAM/CD49f negative SUM229 breast carcinoma subpopulation
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM229 breast carcinoma cell line, EpCAM/CD49f negative subpopulation
treatment: DMSO
|
| Growth protocol |
culture media: F12 supplemented with 5% FBS, 5 µg/ml insulin, 1 µg/ml hydrocortisone, 10 mM HEPES
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using Qiagen DNeasy Blood & Tissue kit and bisulfite conversion of genomic DNA was performed using Zymo Research EZ DNA Methylation kit
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Per InfiniumHDAssay_MethylationProtocolGuide.pdf
|
| |
|
| Hybridization protocol |
Per InfiniumHDAssay_MethylationProtocolGuide.pdf
|
| Scan protocol |
Illumina HiScan
|
| Description |
SUM229neg_DMSO
|
| Data processing |
Methylation fraction (β) values were normalized to Illumina 450K internal controls (90 probe pairs targeting housekeeping genes) and background subtracted according to the manufacturer's protocol using Illumina GenomeStudio v1.8 software.
Genome build: hg19
[450K_betavalues.csv] Linked as supplementary file on Series record. File includes Illumina GenomeStudio v1.8 output including normalized methylation fraction (β) values, methylation Probe IDs, UCSC CpG island coordinates, and UCSC RefGene Name/Group.
|
| |
|
| Submission date |
Sep 21, 2016 |
| Last update date |
Jan 20, 2017 |
| Contact name |
Gary L Johnson |
| E-mail(s) |
glj@med.unc.edu
|
| Organization name |
University of North Carolina School of Medicine
|
| Department |
Pharmacology
|
| Lab |
Gary L. Johnson Lab
|
| Street address |
4009 Genetic Medicine Building, 120 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE87154 |
Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex (DNA methylation) |
| GSE87424 |
Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex |
|
