|
| Status |
Public on Mar 13, 2020 |
| Title |
CLL_A_del17p_untreated_6 |
| Sample type |
genomic |
| |
|
| Source name |
CLL, group A (del(17p) and/or TP53mut, untreated)
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: unknown
predicted_sex_rnbeads_package_in_bioconductor: female
age_years: 71
treated: no
response to therapy: not applicable
ighv_mutation_status: mutated
ighv_mutation_status_as_percentage_homology: 82.62
del13q14: yes
trisomy_12: no
del14q32: no
del11q22: no
del17p13: yes
tp53_mutation: c.527G>C; 528C>T
tp53_mutation_type: missense
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from CD19+ fractions of patients' peripheral blood mononuclear cells (PBMCs) using Qiagen AllPrep Kit according to standard instructions
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChips using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using Illumina iScan reader with standard recommended settings
|
| Data processing |
The raw data were processed using the RnBeads package in R/Bioconductor. Probes known to be cross-reactive (43 230) or overlapping known single-nucleotide polymorphisms (SNPs; 8 704), as well as probes giving unreliable measurements (884 as determined by the Greedycut algorithm) were excluded from analysis. The data from the remaining 432 759 probes were subjected to background subtraction using the Noob method and beta-mixture quantile normalization (BMIQ). This normalization strategy successfully mitigated the inherent bias in β-value distributions between the two different types of probes (Infinium I and II) that are present on the HumanMethylation450 BeadChip. In a subsequent step, probes of non-CpG context (1 251), probes binding to sequences on sex chromosomes (9 917) and probes with low standard deviation (69 867) were filtered out. The data obtained by the remaining 351 724 probes were used in downstream analyses.
|
| |
|
| Submission date |
Sep 02, 2019 |
| Last update date |
Mar 13, 2020 |
| Contact name |
Deyan Yordanov Yosifov |
| E-mail(s) |
deyan.yosifov@uniklinik-ulm.de, deyan.yosifov@gmail.com
|
| Phone |
+4973150045870
|
| Organization name |
University Hospital Ulm
|
| Department |
Internal Medicine III
|
| Street address |
Albert-Einstein-Allee 23
|
| City |
Ulm |
| ZIP/Postal code |
89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE136724 |
DNA methylation of chronic lymphocytic leukemia with differential response to chemotherapy |
|
