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| Status |
Public on Jan 09, 2023 |
| Title |
Expression data from rat prefrontal cortex administrated with MK-801 |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Schizophrenia is a group of severe mental disorders. MK-801 is a common chemical that is used to construct schizophrenic animal model. In the present study, male SD rats were received MK-801 (0.2 mg/kg) intraperitoneal injections for 2 weeks. PFC tissue samples were collected freshly when sacrificing the rats and then quickly frozen and stored under -80°C for RNA sequencing. Differentially-expressed genes (DEGs) were determined by using DESeq2. A total of 129 DEGs, including 50 down-regulated and 79 up-regulated DEGs, were determined. By comparing with the online database TargetScanHuman (Release 8.0) and miRDB (Version 6.0), we found 4 genes (SIK1, TWIST1, BTG2, EGR2) that were altered in the schizophrenic model rat PFC and also are potential targets of miR-25.
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| Overall design |
Male SD rats (aging 21 days and weighing 60 ± 5 g) were randomly assigned into two groups (n = 5 per group). After habituating for 1-week, the two groups received either MK-801 (0.2 mg/kg) or saline (0.9%) intraperitoneal injections for 2 weeks. PFC tissue samples were collected freshly when sacrificing the rats and then quickly frozen and stored under -80°C for RNA sequencing. The RNA-seq test was performed by Novogene (Beijing, China). Briefly, the RNA-seq library for sequencing was prepared by Novogene following the standard Illumina protocols. Reads were aligned to the genome using HISAT2 (Version 2.2.1) and SAMtools (Version 1.15.1) with referencing the gene annotation file from Ensembl (Release 105). FeatureCounts (Subread package Version 2.0.1) was employed to count the reads and then to create the expression matrix. Differentially-expressed genes (DEGs) were determined by using DESeq2 (Version 1.36.0) with P value < 0.05 and |logFC| ≥ 1 as the selection criteria.
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| Contributor(s) |
Pan B, Zhu X, Han B, Weng J, Wang Y, Liu Y |
| Citation(s) |
36744005 |
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| Submission date |
Dec 08, 2022 |
| Last update date |
Feb 10, 2023 |
| Contact name |
Bo Pan |
| E-mail(s) |
bopan@yzu.edu.cn
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| Organization name |
Yangzhou University Medical College
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| Department |
Department of Pharmacy
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| Street address |
No.136, JiangYangZhongLu
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| City |
Yangzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
225001 |
| Country |
China |
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| Platforms (1) |
| GPL25947 |
Illumina NovaSeq 6000 (Rattus norvegicus) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA910095 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE220510_Rat_PFC_RNA-seq_raw_counts.txt.gz |
469.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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