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Sample GSM1253179 Query DataSets for GSM1253179
Status Public on Sep 24, 2014
Title L1236 DNA methylation
Sample type genomic
 
Source name Hodgkin's Lymphoma cell line
Organism Homo sapiens
Characteristics cell line: L1236
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 St├╝beweg 51
City Freiburg
State/province Baden-W├╝rttemberg
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

Data table header descriptions
ID_REF
VALUE Average Beta
Detection_Pval

Data table
ID_REF VALUE Detection_Pval
cg00000029 0.73618 0
cg00000108 0.89776 0
cg00000109 0.89861 0
cg00000165 0.94135 0
cg00000236 0.9157 0
cg00000289 0.56796 0
cg00000292 0.73195 0
cg00000321 0.85584 0
cg00000363 0.93932 0
cg00000622 0.01039 0
cg00000658 0.87429 0
cg00000714 0.13095 0
cg00000721 0.95388 0
cg00000734 0.12112 0
cg00000769 0.05303 0
cg00000807 0.90491 0
cg00000884 0.71154 0
cg00000905 0.17115 0
cg00000924 0.95221 0
cg00000948 0.87023 0

Total number of rows: 485577

Table truncated, full table size 9915 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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