|
| Status |
Public on Jul 01, 2012 |
| Title |
PNET cell line 3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
PNET cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PNET cell line
gender: female
untreated/treated: untreated
|
| Treatment protocol |
treated; 30 nM DAC 72 hours, with addition of 25 nM TSA during the last 48 hours, daily refreshal of culture media containing drugs
|
| Growth protocol |
cultured in DMEM or RPMI at 37 C and 5% CO2 in non-hypoxic conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Using the BioPrime Array-CGH Genomic Labeling kit (Invitrogen, Carlsbad, USA), amino-allyl dUTPs were incorporated into 500ng of the methylated amplicons (generated by DMH) , allowing the amplicons to be labeled with the fluorescent dyes Cy5 (patient samples) and Cy3 (common reference samples).
|
| |
|
| Channel 2 |
| Source name |
[reference] cell line
|
| Organism |
Homo sapiens |
| Characteristics |
reference composition: mix from 5 healthy males and 5 healthy females
|
| Treatment protocol |
treated; 30 nM DAC 72 hours, with addition of 25 nM TSA during the last 48 hours, daily refreshal of culture media containing drugs
|
| Growth protocol |
cultured in DMEM or RPMI at 37 C and 5% CO2 in non-hypoxic conditions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Using the BioPrime Array-CGH Genomic Labeling kit (Invitrogen, Carlsbad, USA), amino-allyl dUTPs were incorporated into 500ng of the methylated amplicons (generated by DMH) , allowing the amplicons to be labeled with the fluorescent dyes Cy5 (patient samples) and Cy3 (common reference samples).
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (the Oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential according to the Agilent protocol.
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
|
| Description |
__251479111557_S01_ChIP-v1_95_May07.txt
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Agilent Feature Extraction Software (v 8.5.1.1) was used for data extraction. The R and Bioconductor statistical environment (version 2.7) were used for quality control and weighed P-spline normalization (package turbotrend). No background correction was performed.
|
| |
|
| Submission date |
Feb 02, 2012 |
| Last update date |
Jul 01, 2012 |
| Contact name |
Floor Duijkers |
| Organization name |
Erasmus MC
|
| Department |
Pediatric Oncology-Hematology
|
| Street address |
Dr. Molewaterplein 50-60 Ee15-02
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 GE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL4126 |
| Series (2) |
| GSE35506 |
Nanomolar treatment with epigenetic drug combination induces genome-wide methylation and expression alterations in neuro-ectodermal cell lines [DNA methylation] |
| GSE35798 |
Nanomolar treatment with epigenetic drug combination induces genome-wide methylation and expression alterations in neuro-ectodermal cell lines |
|
