Comment[GEAAccession]	E-GEAD-399
MAGE-TAB Version	1.1
Investigation Title	Transcriptome dataset of human corneal endothelium
Experiment Description	A transcriptome dataset from ribosomal RNA-depleted total RNA of corneal endothelium from the eyes derived from seven Caucasians without ocular diseases. Cornea endothelium is one of the five different layers (epithelium, Bowman's layer, stroma, Descemet's membrane, and endothelium) of cornea. As corneal endothelium has limited proliferative capacity, damage to corneal endothelium by multiple pathological conditions, such as Fuchs endothelial corneal dystrophy (FECD; OMIM ID: 204870), invasive cataract surgery, glaucoma surgery, and endotheliitis, induce loss of corneal transparency resulting in severe visual disturbance. Therofore, the dataset should be useful for investigating the function/dysfunction of cornea as well as for the extended transcriptome analyses integrated with the data of non-coding RNAs.
Experimental Design	organism part comparison design	quality control testing design
Experimental Factor Name	isolate
Experimental Factor Type	isolate
Person Last Name	Nakano	Tokuda
Person First Name	Masakazu	Yuichi
Person Affiliation	Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine	
Person Roles	submitter	submitter
Public Release Date	2020-12-08
Protocol Name	P-GEAD-660	P-GEAD-661	P-GEAD-662	P-GEAD-663	P-GEAD-664
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Corneal endothelium cells were separated from the other corneal layers of normal Caucasian donor.	Corneal endothelium cells were lysed in QIAzol lysis reagent, and total RNA was extracted by RNeasy Mini Kit following the manufacturer's instructions.	After removed ribosomal RNA, the libraries for total RNA were generated by SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian following the manufacturer's instructions.	The libraries were clustered by TruSeq PE Cluster Kit v3 and sequenced by using a paired-end 100-bp read protocol on a HiScanSQ System with TruSeq SBS Kit v3.	Quality control of short reads was performed using the FastQC 0.11.9. Low-quality bases were removed using fastp 0.20.1 with default setting. Adapter sequences were removed using the Trimmomatic version 0.39 program. After filtering, paired short reads were mapped into human reference genome sequence (GRCh38) by using STAR version 2.7.3a program. The gene expression analysis was performed by RSEM version 1.3.3 and summarized into a file as the matrix data of TPM values.
SDRF File	E-GEAD-399.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB9914
Comment[Last Update Date]	2020-12-08