|
| Status |
Public on Jul 11, 2023 |
| Title |
24_18 sample, chordoma |
| Sample type |
genomic |
| |
|
| Source name |
chordoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: chordoma
Sex: female
age: 43
craniocervical junction: yes
days survival: 1771
alive at censor point: yes
methylation cluster: chordoma_C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA and total RNA from tissue samples were isolated using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). The procedure included tissue homogenizing with rotor stator homogenizer Omni Tissue Master (Omni International). The concentration of samples was measured both spectrophotometrically using NanoDrop 2000 (Thermo Scientific) and with fluorescence-based method using QuantiFluor Dye kit (Promega) and Quantus (Promega) instrument. Isolated total RNA was stored at -80 o C, whereas genomic DNA was stored at -20 o C.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
DNA from 32 skull base chordomas and 4 NP samples were bisulfite converted with EZ-96 DNA Methylation kit (Zymo Research, Orange, CA, USA)
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Data processing |
minfi was utilized to generate beta values and funnorm-normalized m-values (supplementary file). Probes containing SNPs and high p-value were dropped.
|
| |
|
| Submission date |
Apr 20, 2023 |
| Last update date |
Jul 11, 2023 |
| Contact name |
Szymon Piotr Baluszek |
| E-mail(s) |
szymon.baluszek@gmail.com
|
| Organization name |
Maria Sklodowska-Curie National Research Institute of Oncology
|
| Department |
Department of Molecular and Translational Oncology
|
| Street address |
Wilhelma Konrada Roentgena 5
|
| City |
Warsaw |
| State/province |
mazowieckie |
| ZIP/Postal code |
02-781 |
| Country |
Poland |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE230168 |
DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment |
|
