|
| Status |
Public on Jan 01, 2014 |
| Title |
PrEC SFN-3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
MeDIP DNA from PrEC SFN treatment
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PrEC
|
| Treatment protocol |
Cells were treated with 15uM SFN
|
| Growth protocol |
PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors. Cells were used between passage 0 and passage 7
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen), and fragmented using MseI restriction enzyme digestion to yield DNA fragments between 200 to 1,000 bp. Methylated DNA was enriched using methyl-DNA immunoprecipitation (MeDIP) according to manufacturer’s protocol. MeDIP-enriched DNA as well as input DNA was amplified with GenomePlex Complete Whole Genome Amplification kit (Sigma).
|
| Label |
Cy5
|
| Label protocol |
MeDIP and input DNA were labeled using NimbleGen Dual-Color DNA Labeling Kit per manufacturer's protocol. MeDIP DNA was labeled with Cy5, input DNA was labeled with Cy3
|
| |
|
| Channel 2 |
| Source name |
Input DNA from PrEC SFN treatment
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PrEC
|
| Treatment protocol |
Cells were treated with 15uM SFN
|
| Growth protocol |
PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors. Cells were used between passage 0 and passage 7
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen), and fragmented using MseI restriction enzyme digestion to yield DNA fragments between 200 to 1,000 bp. Methylated DNA was enriched using methyl-DNA immunoprecipitation (MeDIP) according to manufacturer’s protocol. MeDIP-enriched DNA as well as input DNA was amplified with GenomePlex Complete Whole Genome Amplification kit (Sigma).
|
| Label |
Cy3
|
| Label protocol |
MeDIP and input DNA were labeled using NimbleGen Dual-Color DNA Labeling Kit per manufacturer's protocol. MeDIP DNA was labeled with Cy5, input DNA was labeled with Cy3
|
| |
|
| |
| Hybridization protocol |
Sample hybridization were done using Nimblegen Hybridization System 4 (Roche)
|
| Scan protocol |
Array scanning were done using Axon GenePix Pro 4200A (Molecular Device)
|
| Description |
MeDIP-chip PrEC SFN 48h
|
| Data processing |
Arrays were processed using Nimblegen's standard default protocol for Nimblescan data extraction. Attached .gff files with scaled, log2 (ChIP/Input) ratio.
|
| |
|
| Submission date |
May 16, 2013 |
| Last update date |
Jan 01, 2014 |
| Contact name |
Carmen Wong |
| E-mail(s) |
carmen.wong@oregonstate.edu
|
| Phone |
541-737-4189
|
| Organization name |
Oregon State University
|
| Department |
Biological and Population Health Sciences
|
| Lab |
Emily Ho
|
| Street address |
103 Milam Hall
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL17148 |
| Series (1) |
| GSE47017 |
MeDIP-Chip of PrEC, LnCAP, and PC3 cells treated with vehicle control, sulforaphane, or 3,3’-diindolylmethane |
|
