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Sample GSM6781637 Query DataSets for GSM6781637
Status Public on Apr 30, 2023
Title 50_1: blood_FECD_noexp_3
Sample type genomic
 
Source name whole blood DNA
Organism Homo sapiens
Characteristics gender: male
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: 10
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) lo.skorodumova@gmail.com
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

Supplementary data files not provided
Processed data are available on Series record

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