|
| Status |
Public on Apr 30, 2023 |
| Title |
Dfu_29: blood_FECD_noexp_17 |
| Sample type |
genomic |
| |
|
| Source name |
whole blood DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
age: 76
condition: Fuchs endothelial corneal dystrophy
ctg18.1 repeats expansion status: non expanded
number of ctg repeats on the smaller allele: 10
number of ctg repeats on the greater allele: 13
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from thawed blood samples with the Wizard® Genomic DNA Purification Kit (Promega Corp.; Wisconsin, USA) or Gentra Puregene Blood Kit (Qiagen; Germany) according to the manufacturer's protocol.
|
| Label |
Cy3, Cy5
|
| Label protocol |
200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using Multi-Sample Amplification 1 Mix (WG-MA1), Random Primer Mix (WG-RPM) and Multi-Sample Amplification Master Mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).
|
| |
|
| Hybridization protocol |
RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
|
| Scan protocol |
After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a iScan array scanner (Illumina).
|
| Description |
Genomic DNA extracted from whole blood was genotyped using Infinium Omni2.5-8 v1.5 Kit (Illumina). Diagnosis, group assignment and CTG18.1 genotyping were conducted according to methods described in Skorodumova et al. (2018; doi: 10.1167/iovs.18-24590).
|
| Data processing |
Genomic DNA was genotyped using Infinium Omni2.5-8 v1.5 Genotyping BeadChips (Illumina).
Image data was analyzed using GenomeStudio 2.0.4 with Genotyping module 2.0.4 (Illumina).
|
| |
|
| Submission date |
Dec 02, 2022 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Liubov Skorodumova |
| E-mail(s) |
[email protected]
|
| Organization name |
Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency
|
| Lab |
Human Molecular Genetics
|
| Street address |
Malaya Pirogovskaya st., 1A
|
| City |
Moscow |
| ZIP/Postal code |
119435 |
| Country |
Russia |
| |
|
| Platform ID |
GPL32909 |
| Series (1) |
| GSE219272 |
Study of variants associated with Fuchs corneal endothelial dystrophy cases without expansion of CTG18.1 repeats |
|
