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| Status |
Public on Feb 23, 2017 |
| Title |
Transcriptome analyses of cerebral ischemia reveal functional lncRNAs in ischemia stroke |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Background and Purpose: Long noncoding RNAs (lncRNAs) are an emerging class of genomic regulatory molecules reported in neurodevelopment and many diseases. Despite extensive studies have identified lncRNAs and discovered their functions in CNS diseases, the function of lncRNAs in ischemia stroke remains poorly understood.
Method: Ischemia was induced by transient middle cerebral artery occlusion. Expression profiles of lncRNAs, miRNAs and mRNAs after ischemia stroke were obtained using high throughput sequencing technology. A correlation network was constructed to predict lncRNA functions. LncRNA-miRNA-mRNA network was constructed to discover ceRNAs.
Results: 1924 novel lncRNAs were identified, indicating that the ischemia stroke has a complex effect on lncRNAs. The top 10 regulated lncRNAs was validated by qRT-PCR. We have also predicted function of lncRNAs, and subjected them to gene co-expression network analysis, revealing the involvement of lncRNAs in many important biological process including injury and repair that are implicated in the regulation of ischemia stroke. Furthermore, lncRNAs mediated SMD (Staufen1-mediated mRNA decay) was analyzed and ceRNA (competitive endogenous RNAs) network was constructed in ischemia stroke.
Conclusions: This study reports the genome-wide lncRNA profiles in ischemia stroke using high throughput sequencing and constructs a systematic lncRNA-miRNA-mRNA network which reveals a complex functional noncoding RNA regulatory network in ischemia stroke.
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| Overall design |
Rat brain mRNA, miRNA, lncRNA profiles after 24 hours of middle cerebral artery occlusion (MCAO) were generated by deep sequencing, 5 biological replicates, using Illumina HiSeq 2500.
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| Contributor(s) |
Liu J, Zhang K, Deng Z |
| Citation(s) |
29516010 |
| Submission date |
Feb 23, 2016 |
| Last update date |
Aug 27, 2019 |
| Contact name |
Kunshan Zhang |
| E-mail(s) |
mart555@163.com
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| Organization name |
Tongji Hospital, Tongji University
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| Department |
Stem cell Translational Research center
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| Street address |
389 Xincun Road
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platforms (1) |
| GPL18694 |
Illumina HiSeq 2500 (Rattus norvegicus) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA312916 |
| SRA |
SRP070695 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE78200_fpkm.csv.gz |
1019.6 Kb |
(ftp)(http) |
CSV |
| GSE78200_novel.lncRNA.bed.gz |
57.2 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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