|
| Status |
Public on Oct 01, 2019 |
| Title |
L2 |
| Sample type |
genomic |
| |
|
| Source name |
genomic DNA from L2 Blood (mother of proband)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
gender: F
sentrixid_sentrixposition: 202908540141_R02C01
age: 51
disease state: Normal
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from peripheral blood lymphocytes by using the salting-out method.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard llumina Protocol
|
| |
|
| Hybridization protocol |
800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.
|
| Scan protocol |
Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)
|
| Description |
methylation profiling using bisulfite converted
|
| Data processing |
Data was analysed using R version 3.4.1 (2017-06-30). Beta-values were extracted from ‘idat’ files by using the ‘Load’ module of the ‘Champ’ R package (v. 2.12.0), with quality control options set as default. The quality control step retained 759772 probes, which were used for further analysis. Probes overlapped with SNP (79662) and with a detection pvalue < 0.01 (3447), beadcount <3 in at least 5% of samples in one or more samples (2582) were eliminated. X or Y chromosomes probes (17432), non-cg probes (2915), and probes aligning to multiple locations (46) and unannotated probes were also removed from analysis. No background correction was carried out. SWAN normalisation was applied, with the ‘method’ option set to “minfi”. The SWAN normalized samples were assigned with respective genome coordinates based on probe name and manifest file (Illumina Inc., USA).
The file 'matrix_signal_intensities.txt' includes: Unmethylated signal (B) and methylated signal (A) intensities
|
| |
|
| Submission date |
Jul 03, 2019 |
| Last update date |
Oct 02, 2019 |
| Contact name |
Ankit Verma |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)
|
| Street address |
Via Pietro Castellino, 111
|
| City |
Naples |
| State/province |
Naples |
| ZIP/Postal code |
80131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE133774 |
Clinical spectrum of multi-locus imprinting disturbances associated with maternal-effect variants range from overt Beckwith-Wiedemann syndrome to apparently healthy phenotype |
|
