|
| Status |
Public on Dec 07, 2013 |
| Title |
non Side Population rep1 |
| Sample type |
genomic |
| |
|
| Source name |
DLBCL Cell line OCI Ly3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OCI Ly3
phenotype: non side population
dlbcl subtype: ABC
|
| Treatment protocol |
Cells were stained with 10µg/ml Hoechst33342 for 90min in 37°C. Afterwards cells were washed twice in PBS. FACS analysis showed a pattern of Side Population an Non Side Population cells whcih were sorted separately.
|
| Growth protocol |
DLBCL Cell Line OCI Ly3 was cultured in IMDM medium containing 20% FCS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA of Side Population and Non Side Population cells was extracted using Qiagen® DNA extraction Kit according to the manufacturer's instructions.
|
| Label |
biotin / DNP
|
| Label protocol |
After extraction of gDNA, bisulfite treatment was performed to convert the unmethylated cytosine into uracil. The bisulfite treated DNA is subjected to whole genome amplification (WGA) via random hexamer priming and Phi29 DNA polymerase, which has a proofreading activity resulting in error rates 100 times lower than the Taq polymerase. The products are then enzymatically fragmented, purified from dNTPs, primers and enzymes, and applied to the chip
|
| |
|
| Hybridization protocol |
200 ng DNA was applied per BeadChip according to the manufacturer’s instructions.
|
| Scan protocol |
BeadChips were scanned using a Illumina Bead Array Reader®
|
| Data processing |
Initial data analysis was performed with the BeadStudio Methylation Module. DNA methylation values, described as beta values, were recorded for each locus in each sample. Only few CpG sites did not reveal reliable signals, as determined by their detection P-value, and were therefore excluded from further analysis. Raw data were quantile normalized. Statistical analysis and clustering by Euclidian distance was performed using the MultiExperiment Viewer (MeV, TM4)
|
| |
|
| Submission date |
Dec 05, 2013 |
| Last update date |
Dec 07, 2013 |
| Contact name |
Raphael Koch |
| E-mail(s) |
raphael.koch@med.uni-goettingen.de
|
| Organization name |
University Medicine of Goettingen
|
| Department |
Hematology
|
| Street address |
Robert Koch Str
|
| City |
Goettingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE53043 |
Methylation status of OCI Ly3 SP vs. nonSP |
| GSE53079 |
OCI Ly3 SP vs. nonSP cells |
|
