|
Status |
Public on Jul 01, 2012 |
Title |
NBL 3 cell line |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
NBL cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: NBL 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 |
__251479111660_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.
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|
|
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 |
|