|
| Status |
Public on Mar 24, 2015 |
| Title |
genomic DNA from S4 48 PD |
| Sample type |
genomic |
| |
|
| Source name |
Pre-crisis T-cell culture
|
| Organism |
Homo sapiens |
| Characteristics |
tissue/cell type: Pre-crisis T-cell culture
sample type: cell culture
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted according to standard protocols and DNA purity and concentration determined by spechtrophotometry.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA (EZ DNA methylation gold) was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol.
|
| Scan protocol |
Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting
|
| Description |
S4 48 PD
Pre-crisis cell culture sample
|
| Data processing |
GenomeStudio software v2010.3 with the Methylation module. Intergenic CpG-sites, CpG-sites at chromosome X and Y, Detection P-value > 0.05 and nbeads<=3 were filtered (set to NA). Probe type normalization was performed using the BMIQ Method.
|
| |
|
| Submission date |
Mar 20, 2014 |
| Last update date |
Mar 24, 2015 |
| Contact name |
Sofie Degerman |
| E-mail(s) |
sofie.degerman@umu.se
|
| Organization name |
Umeå University
|
| Department |
Medical Biosciensces
|
| Lab |
Pathology
|
| Street address |
NUS, Blg 6M, 2nd floor
|
| City |
Umeå |
| State/province |
Sweden |
| ZIP/Postal code |
90185 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE56068 |
Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias [methylation] |
| GSE56070 |
Immortalization of T-cells is accompanied by gradual changes in CpG methylation resulting in a profile resembling a subset of T-cell leukemias |
|
