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| Status |
Public on Oct 01, 2020 |
| Title |
VEH control group_2 |
| Sample type |
SRA |
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| Source name |
VEH control group
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: hippocampus
strain: Sprague-Dawley
age: post natal day 21
treatment: VEH control
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| Treatment protocol |
This study used 3 groups (10 rats/group) Sprague-Dawley rats. Thirty rats were randomly assigned to three groups, VEH control group (n = 10), MK-801 group (n = 10) and MK-801+CLO group (n = 10). Rat model of schizophrenia was induced by MK-801 intraperitoneal injection. Each rat in the MK-801 and MK-801+CLO groups received an intraperitoneal injection of 0.2 mg/kg of MK-801 once a day for 14 consecutive days. 0.2 mg/kg MK-801 has been demonstrated to induce schizophrenia-like structural changes in rat hippocampus and regulate multiple steps of hippocampal neurogenesis. Ten control animals received an equal volume of sterile saline for 14 and 7 days. After treating with MK-801 for 14 consecutive days, MK-801 group were intraperitoneally in an equal volume of sterile saline for additional 7 days, the third group (MK-801+CLO) rats were administered intraperitoneally in 10mg/kg dose for additional 7 days.
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| Growth protocol |
Rats were housed two or three to a clear polycarbonate cages under a controlled 12/12-h light-dark cycle (light from 7:00 AM to 7:00 PM), with room temperature at 23±1 °C and humidity at 55±5% in Guangdong Medical University Experimental Animal Center. The rats were continuously given free access to food and water. After 14 days of habituation to the age 5 weeks (120-140 g), rats were used in the subsequent drug treatment and experiments.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were rapidly removed and each hippocampus was dissected, frozen immediately in liquid nitrogen, then stored at -80°C refrigerator until needed. Total RNA was extracted from the frozen tissues using the AMBION RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s protocol. Subsequent RNA purification was performed using the Qiagen RNeasy® Kit (Qiagen, Mainz, Germany). RNA quality was confirmed using the Agilent 2100 Bioanalyzer system after purification (Agilent Technologies, Inc., Santa Clara, CA).
miRNA libraries were prepared for sequencing using standard Illumina protocols
Small RNA next generation sequencing
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Sample_F054
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| Data processing |
Illumina Casava1.7 software used for basecalling.
After removing low-quality reads and reads without the 3’ adaptor and 5’adaptor-contaminant by Cutadapt (Version 1.14) software, keep Q20 reads (>80%) according to fastx_toolkit (Version 0.0.13) software, removing the reads with N bases according to NGSQCToolkit (Version 2.3.3) software.
Subsequently, the remaining clean reads counted and analyzed by software (such as fastx_toolkit, bowtie, OE reads Statistical tool, DESeq). The clean reads were compared against the Rfam, GeneBank and Repbase databases to remove rRNAs, tRNAs, small nuclear RNA (snRNA) and other non-coding RNAs.
The remnant reads were searched against miRbase (version21; http://www.mirbase.org/) to identify known miRNAs for further analysis. After identifying the known miRNAs, unannotated sequences that were not assigned to any above databases were used for the prediction of novel miRNAs by miRDeep2.
Additionally, their hairpin structures were then analyzed using the RNAfold software. We predicted differentially expressed miRNA target genes according to TargetScan, miRDB, RNAhybrid and Miranda algorithms in miRwalk2.0 online website.
To assess the prospective functions of the most significant differently miRNAs, we discharged GO-term functional enrichment analysis of biological processes and KEGG pathways using DAVID (Database for Annotation, Visualization, and Integrated Discovery).
Genome_build: Rnor_6.0 (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000001895.5_Rnor_6.0/GCF_000001895.5_Rnor_6.0_genomic.fna.gz)
Supplementary_files_format_and_content: tab-delimited text file includes raw and TPM values for each Sample
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| Submission date |
Apr 08, 2019 |
| Last update date |
Oct 01, 2020 |
| Contact name |
hui Wen Huang |
| E-mail(s) |
hwh553836258@126.com
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| Phone |
13535544606
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| Organization name |
Jinan University
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| Street address |
Huang pu da dao West 601
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| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
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| Platform ID |
GPL22396 |
| Series (1) |
| GSE129466 |
Effects of the Co-Administration of MK-801 and Clozapine on MiRNA Expression Profiles in Rats |
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| Relations |
| BioSample |
SAMN11357876 |
| SRA |
SRX5653753 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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