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| Status |
Public on Feb 24, 2020 |
| Title |
RNA sequencing facilitates quantitative analysis of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells transcriptomes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We report the application of Illumina paired-end RNA-seq approach for transcriptome of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells . By removing sequence-dependent bias and amplification noise using UMI-tools. The mapped reads of each sample were assembled using StringTie. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. By obtaining a total of million paired-end reads of sequence from neural stem cells , we generated transcriptome profiles of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells , respectively. We found 201 differentially expressed genes (DEGs) between siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells. This study provides a detailed analysis of the underlying mechanisms of strokeļ¼such as neuronal injury and long-term effect, generated by RNA-seq technology.
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| Overall design |
Transcriptome profiles of siRNA circHIPK2 transfected neural stem cells and siRNA circCon transfected neural stem cells, respectively, were generated by paired-end sequencing, in triplicate, using Illumina Novaseq 6000.
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| Contributor(s) |
Yao H, Wang G |
| Citation(s) |
32062357 |
| Submission date |
Jul 02, 2019 |
| Last update date |
Feb 24, 2020 |
| Contact name |
guangtian wang |
| E-mail(s) |
wangguangtian0451@163.com
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| Organization name |
School of Medicine, Southeast University
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| Department |
Department of Pharmacology
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| Street address |
Dingjiaqiao 87
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| City |
Nanjing |
| ZIP/Postal code |
210009 |
| Country |
China |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA552285 |
| SRA |
SRP212771 |
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