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| Status |
Public on Mar 08, 2012 |
| Title |
EBV-LCL, individual 7, array 6 |
| Sample type |
genomic |
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| Source name |
EBV-LCL, individual 7
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| Organism |
Homo sapiens |
| Characteristics |
cell type: EBV-transformed lymphocyte cell line (EBV-LCL)
individual: 7
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from whole blood and the EBV-LCLs.
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| Label |
biotin
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| Label protocol |
Following the manufacturers’ protocols, DNA was fragmented with MseI to a median size of 500 bp and the methylome was enriched for using MethylMiner (Invitrogen, Carlsbad, CA, USA) and further amplified using the Sigma WGA2 kit (Sigma-Aldrich, St. Louis, MO, USA). The amplified methylomes were fragmented using the Affymetrix (Santa Clara, CA, USA) 6.0 fragment reagents and labeled using the Affymetrix WT-ds DNA Terminal labeling kit.
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| Hybridization protocol |
DNA was hybridized to the Affymetrix GeneChip® Human Tiling 2.0R array set overnight. The following day, the arrays were washed according to the manufacturer's protocol.
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| Scan protocol |
The arrays were scanned according to the manufacturer's protocol.
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| Description |
Sample 021
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| Data processing |
The data was background-corrected using the robust multi-array (RMA) procedure, which models the probe intensities as signal plus noise, assuming exponential distribution for the signal and normal distribution for the noise (Irizarry RA, Hobbs B, Collin F et al: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003; 4: 249-264.). Next, we used quantile normalization, which first sorts the probe intensities for each individual array and then averages across all arrays. Finally, to obtain the normalized results for any particular array, we re-order the averages obtained above so as to match the original ordering of the probe intensities on the array (Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003; 19: 185-193.).
Background-corrected and quantile-normalized data is provided for all 30 samples per chromosome. The files are available as supplementary files on the GSE35204 record.
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| Submission date |
Jan 18, 2012 |
| Last update date |
Mar 08, 2012 |
| Contact name |
Karolina A Aberg |
| Organization name |
Virginia Commonwealth University
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| Department |
Center for Biomarker Resarch & Personalized Medicine
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| Street address |
1112 East Clay Street
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| City |
Richmond |
| State/province |
VA |
| ZIP/Postal code |
23298 |
| Country |
USA |
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| Platform ID |
GPL4915 |
| Series (1) |
| GSE35204 |
Methylome-wide comparison of human genomic DNA extracted from whole blood and from EBV-transformed lymphocyte cell lines |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM863649_S0021-HuTF.CEL.gz |
24.5 Mb |
(ftp)(http) |
CEL |
| Processed data are available on Series record |
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