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Sample GSM1253181 Query DataSets for GSM1253181
Status Public on Sep 24, 2014
Title Reh DNA Methylation
Sample type genomic
Source name Pro-B lymphoblastic leukemia cell line
Organism Homo sapiens
Characteristics cell line: Reh
cell type: Pro-B lymphoblastic leukemia
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 ( 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
Phone +49 (0)761 270-77576
Organization name University Medical Center Freiburg
Department Zentrum für Translationale Zellforschung
Lab AG Onco-Immunology
Street address Breisacher Str. 115
City Freiburg
State/province Baden-Württemberg
ZIP/Postal code 79106
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
VALUE Average Beta

Data table
ID_REF VALUE Detection_Pval
cg00000029 0.91003 0
cg00000108 0.94232 0
cg00000109 0.91139 0
cg00000165 0.94405 0
cg00000236 0.91629 0
cg00000289 0.68182 0
cg00000292 0.81162 0
cg00000321 0.82627 0
cg00000363 0.93432 0
cg00000622 0.00994 0
cg00000658 0.82664 0
cg00000714 0.1742 0
cg00000721 0.95223 0
cg00000734 0.07875 0
cg00000769 0.05431 0
cg00000807 0.82649 0
cg00000884 0.85355 0
cg00000905 0.12549 0
cg00000924 0.90119 0
cg00000948 0.92608 0

Total number of rows: 485577

Table truncated, full table size 9914 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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