|
| Status |
Public on Sep 24, 2020 |
| Title |
DNA methylation from T-ALL ALL_0001 EPICarray |
| Sample type |
genomic |
| |
|
| Source name |
Blast from the bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blast from the bone marrow
disease state: T-ALL
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted by a SDS-containing lysis buffer containing proteinase K and purified by isopropanol precipitation. 250ng of DNA was used for bisulfite conversion by the EZ DNA methylation Kit (Zymo Research).
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Infinium HumanMethylationEPIC BeadChip (Illumina) using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Data processing |
RnBeads.hg19 in R (versions >3.4). β values were obtained after filtering and normalization using the default preprocessing pipeline.
Normalized (RnBeads, SWAN normalization) Average Beta
|
| |
|
| Submission date |
Jul 29, 2020 |
| Last update date |
Jul 13, 2023 |
| Contact name |
Juliette Roels |
| E-mail(s) |
roels.juliette@gene.com
|
| Phone |
6505807476
|
| Organization name |
Genentech
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL23976 |
| Series (2) |
| GSE155333 |
Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [EPICarray_109TALL] |
| GSE155339 |
Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia |
|
