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Series GSE114896 Query DataSets for GSE114896
Status Public on Feb 02, 2021
Title seekCRIT: detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary Recently, it has been demonstrated that genomes of many species express single stranded RNAs with covalently closed ends, named circular RNAs. Their regulatory potential and functional relevance are just starting to be revealed. Here we present a novel computational tool, seekCRIT (seek for differentially expressed Circular RNAs In Transcriptome), that identifies circular RNAs and detects their differential expression between two conditions. Using seekCRIT we identified the circular RNAs that are expressed in the neural retina and determined that the majority of them (74%) are expressed in both, ischemic and normal conditions. We identified over 40 circular RNAs that were differentially expressed between both conditions and validated these experimentally using qRT-PCR. The high validation rate of 90% with a false discovery rate (FDR) of < 5% demonstrates the accuracy and reliability of seekCRIT.
 
Overall design RNA from rat’s retina was extracted using the RNeasy Lipid Tissue Mini Kit. Two retinal samples were sequenced: a sample subjected to ischemia-reperfusion (IR) injury and collected 12 hours after the reperfusion (IR12) and a control sample (CTRL) subjected to a sham-procedure. 350ng of total RNA samples was used for RNA-seq library preparation using the TruSeq™ Stranded mRNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina). Single-end 150 bp reads were generated on a NextSeq 550 sequencer.
 
Contributor(s) Park JW, Cooper N
Citation(s) 33079938
Submission date May 24, 2018
Last update date Feb 08, 2021
Contact name Jae Yeon Hwang
E-mail(s) wodus0515@gmail.com
Phone 8013185877
Organization name University of Louisville
Department Division of Medical Oncology & Hematology
Street address 505 S. Hancock Street
City Louisville
State/province Kentucky
ZIP/Postal code 40202
Country USA
 
Platforms (1)
GPL25029 NextSeq 550 (Rattus norvegicus)
Samples (2)
GSM3154158 CTRL
GSM3154159 IR12
Relations
BioProject PRJNA472991
SRA SRP148901

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE114896_IR12.data.FPKMs.txt.gz 775.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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