Dataset on transcriptome profiling of corneal endothelium from patients with Fuchs endothelial corneal dystrophy

Fuchs endothelial corneal dystrophy (FECD) is a bilateral inherited eye disease with advanced forms only treatable by corneal transplantation. The pathogenesis of FECD has not been worked out yet, however, trinucleotide repeat polymorphism CTG18.1 in the TCF4 gene has recently been associated with late-onset FECD. Gene expression profiling of corneal endothelium with and without this expansion can help elucidate molecular mechanisms of the disease development. Current data article represents whole transcriptome profiles of corneal endothelium obtained from 12 patients with FECD and 6 control tissues from eye bank donors. RNA sequencing data is available at NCBI Sequence Read Archive under Accession No. PRJNA524323. In addition, each patient and donor were genotyped for CTG18.1 expansion and the corresponding numbers of CTG repeats in the TCF4 gene are provided within this article. The dataset includes samples from FECD patients both with and without CTG18.1 expansion.


Data
The dataset contains raw sequencing data obtained through the transcriptome sequencing of corneal endothelium from 12 patients with FECD and 6 donors. The data files (reads in FASTQ format) were deposited at NCBI SRA database under project accession No. PRJNA524323. Information about tissue samples collected from patients with FECD and control samples from donors is presented in Table 1 and Table 2, respectively.
All patients and donors were also characterized by genotyping for trinucleotide repeat polymorphism CTG18.1 in the TCF4 gene (Table 3).

Ethical statements
This study was approved by the Institutional Review Board of The S. Fyodorov Eye Microsurgery Federal State Institution and was carried out in accordance with The Code of Ethics of the World Medical Association (Declaration of Helsinki).

Collection of tissue and blood samples from FECD patients
Samples of corneal endothelium were obtained from patients diagnosed with FECD and undergoing corneal transplantation at The S. Fyodorov Eye Microsurgery Federal State Institution. All patients included in this study had signed an informed consent form. Table 2 summarizes information about   Specifications table   Subject area  Biology  More specific subject area  Fuchs endothelial corneal dystrophy  Type of data  Text (FASTQ sequence files), Value of the Data The dataset represents transcriptomes of samples from FECD patients as well as from control donors which can be compared to reveal molecular pathways altered in corresponding endothelial cells leading to their accelerated death. The identification of affected metabolic and signaling pathways may indicate the direction of research for the development of specific non-surgical treatment of FECD. All subjects in this study have already been genotyped for CTG18.1 expansion. The dataset includes samples from patients both with and without the expansion, which can be valuable for identifying the role this genetic variation plays in FECD pathogenesis. Expression profiles are available in the form of raw sequencing reads that can be further processed by researchers using their own bioinformatic algorithms and analyzed together with their own data.    [1]. During the endothelial keratoplasty procedure, circular descemetorhexis with a diameter of 7e8 mm was performed using a special hook to obtain samples of corneal endothelium/Descemet's membrane (CEC-DM) complex. RNA in CEC-DM complex was stabilized using RNAlater solution (ThermoFisher Scientific, USA) according to the manufacturer's instructions. Venous blood (4e6 mL) was collected from each patient into vacutainer tubes with EDTA (Becton Dickinson, USA). Blood samples were stored at À20 C prior to DNA extraction.

Collection of control tissue samples from donors
Control samples of corneal endothelium were collected at the Eye Bank of The S. Fyodorov Eye Microsurgery Federal State Institution. Donor samples were selected from those not suitable for corneal transplantation. Information about control tissue samples collected from donors is presented in Table 3.
The eyeball was stored for a maximum of 1 day before extraction of the corneoscleral disc which then was kept in a preservative medium for the period of up to 12 hours. The preservative medium contained: 25% of medium 199, 25% of F-10 medium, 45.3% of DMEM, 2% dextran, 2.7% chondroitin sulfate, gentamicin sulfate 0.00014%, amphotericin B 0.00015%. Afterward, the corneoscleral disc was placed in an artificial anterior chamber endothelial side up. Circular excision of CEC-DM complex 7e8 mm in diameter was performed using spatula and tweezers. After isolation, the donor CEC-DM complexes were immediately immersed in the RNAlater solution (ThermoFisher Scientific, USA). Iris samples were also collected from donors for the TCF4 repeats expansion genotyping.

CEC density measurement
The density of corneal endothelial cells was measured using Tomey EM-3000 Specular Microscope (Tomey, USA). The shooting method was non-contact, the measurement mode was manual/automatic, the shooting area was 0.25 mm Â 0.54 mm with 7 capture points (central þ 6 points on the periphery). The accuracy of corneal thickness measurement was ±10nm ". CEC density was evaluated if at least one of the capture points had enough transparency for the analysis.

DNA extraction
DNA was isolated from thawed blood samples with Gentra Puregene Blood Kit (Qiagen, Germany) according to the manufacturer's protocol. DNA was resuspended in a low TE buffer to a final concentration of 10 ng/ml. DNA from iris samples was extracted using ZR Genomic DNA Tissue MiniPrep (Zymo Research, USA).

Genotyping
Identification of the number of CTG repeats within the CTG18.1 allele in the TCF4 gene was carried out using short tandem repeat (STR) and triplet primed PCR (TP-PCR) techniques exactly according to the procedure described in Ref. [1]. The TCF4 allele was classified as expanded if the number of CTG repeats was !40 according to previously reported literature [2,3].

RNA extraction
Disruption and homogenization of tissue samples were performed with TissueRuptor II (Qiagen, Germany). The time of homogenization was 20 seconds. Total RNA was isolated using RNeasy Micro Kit (Qiagen) following the manufacturer's protocol. Traces of DNA were removed with TURBO DNA-free Kit (ThermoFisher Scientific). RNA concentration was assessed using the Qubit 2 instrument (Invitrogen, USA) with Qubit HS RNA Assay Kit (ThermoFisher Scientific, USA). The quality of total RNA expressed as RNA Integrity Number (RIN) was determined with Bioanalyzer 2100 instrument (Agilent, USA) using an