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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 22, 2022 |
| Title |
RNA sequencing of ipsilateral cortex after transient focal ischemia in mice |
| 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 brain tissue in mice. 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 cerebral cortex tissue, we generated transcriptome profiles of mouse ischemic cortex in sham, 24 h after focal ischemia, 28 d after focal ischemia, with or without neuron-specific knockdown of TIPARP, respectively. We found 2017 differentially expressed genes (DEGs) between Sham+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-Con group, and 516 DEGs between tMCAO+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-TIPARP group at 24 h after stroke. In addition, we found 487 DEGs between Sham+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-Con group, and 192 DEGs between tMCAO+AAV-SYN-shRNA-Con and tMCAO+AAV-SYN-shRNA-TIPARP group at 28 d after stroke. This study provides a detailed analysis of the underlying mechanisms of neuron-specific knockdown of TIPARP in neuronal injury and long-term effect, with biologic replicates, generated by RNA-seq technology.
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| Overall design |
Transcriptome profiles of mouse ischemic cortex in sham, 24 h after focal ischemia, 28 d after focal ischemia, with or without neuron-specific knockdown of TIPARP treatment, respectively, were generated by paired-end sequencing, in triplicate, using Illumina Hiseq 4000.
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| Contributor(s) |
Yao H, Wu F |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 23, 2019 |
| Last update date |
May 22, 2022 |
| Contact name |
Fangfang Wu |
| E-mail(s) |
fangfang.wu@seu.edu.cn
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| Organization name |
Southeast University
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| Department |
Department of Pharmacology
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| Street address |
Dingjia Qiao 87#
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210009 |
| Country |
China |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA544489 |
| SRA |
SRP199339 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE131712_1_genes_fpkm_expression.txt.gz |
7.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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