|
| Status |
Public on Sep 24, 2014 |
| Title |
L428 DNA methylation |
| Sample type |
genomic |
| |
|
| Source name |
Hodgkin's Lymphoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: L428
cell type: Hodgkin's Lymphoma
passages: 7
|
| Treatment protocol |
N/A
|
| Growth protocol |
Cells lines from Hodgkin's lymphoma (L1236 and L428), Pro-B lymphoblastic leukemia (Reh) and Burkitt's lymphoma (Namalwa) were grown in IMDM medium containint 10% FCS, penicillin 100 U/mL, and streptomycin 50 pg/mL and incubated at 37C in a humidified atmosphere containing 5% CO2, with cell densities kept under 5x105 per ml
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Phenol-choroform
|
| Label |
Biotin, DNP
|
| Label protocol |
HumanMethylation 450K BeadChip
|
| |
|
| Hybridization protocol |
HumanMethylation 450K BeadChip
|
| Scan protocol |
HumanMethylation 450K BeadChip
|
| Data processing |
For the analysis of methylation sample data, image scanning, processing, feature extraction and normalization were performed in Illumina GenomeStudio. All intensities are combined in the TPS1928_SampleMethylationProfile_FinalReport_20Jun11_HL_NHL.txt file. Higher-level analysis was performed in R using IMA (https://www.rforge.net/IMA/index.html) followed by a custom R pipeline where probe methylation levels were aggregated per promoter. Promoter methylation fold changes were computed as log2 ratios
|
| |
|
| Submission date |
Oct 28, 2013 |
| Last update date |
Sep 24, 2014 |
| Contact name |
Pierre Daniel Cauchy |
| E-mail(s) |
cauchy@ie-freiburg.mpg.de
|
| Phone |
+49 (0)761 5108-730
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Department of Cellular and Molecular Immunology
|
| Lab |
Laboratory Rudolf Grosschedl
|
| Street address |
Stübeweg 51
|
| City |
Freiburg |
| State/province |
Baden-Württemberg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE51813 |
DNA Methylation in Hodgkin's and non-Hodgkin's lymphoma |
| GSE51814 |
Genome-wide DNase-Seq and methylation profiles in Hodgkin's and non-Hodgkin's lymphoma |
|
