|
| Status |
Public on Sep 15, 2022 |
| Title |
rat_7-week-old-2VO_rep2 [V2] |
| Sample type |
SRA |
| |
|
| Source name |
cerebral cortex
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
treatment: bilateral common carotid artery occlusion
|
| Treatment protocol |
Rats were anesthetized with 2% sodium pentobarbital administered intraperitoneally (30mg/kg). The surgery gently separated the bilateral common carotid arteries permanently ligated with 5-0 silk thread. Rats in the sham group underwent the same procedure with the exception of arterial ligation. Each group contained three rats. The cerebral cortex was collected after the Morris water maze test and quickly preserved in liquid nitrogen.
|
| Growth protocol |
All the animals were housed under a 12-h light-dark cycle (lights on 8 a.m.) at 25°C and 60 ± 10% humidity and given ad libitum access to food and water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Total RNA Extractor (Trizol) kit (B511311, Sangon, China) according to the manufacturer’s protocol
A total amount of 2 g RNA per sample was used as input material for the RNA sample preparations. Next, miRNA sequencing libraries were constructed using TruSeq Small RNA Sample Prep Kits (RS-200-0024, Illumina, USA) following manufacturers recommendations. The library quality was assessed on the Agilent Bioanalyzer 2100 system. mRNA sequencing libraries were constructed from six total RNA samples using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601-02, Vazyme, China)
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
gene expression
|
| Data processing |
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.
Cutadapt V1.14 was used to remove adaptors (cutoff value Q lower than 20). The clean reads were obtained by using Trimmomatic V0.36 after removing low-quality bases at both ends. Reads were compared with the reference genome via miRBase database.
DESeq2 (version 1.12.4) was used to determine differentially expressed genes (DEGs) between two samples. Genes were considered as significant differentially expressed if q-value <0.001 and |FoldChange| >2.
Assembly: the rats reference genome (http://asia.ensembl.org/ index.html)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 03, 2022 |
| Last update date |
Sep 15, 2022 |
| Contact name |
Kaiyue Zhao |
| E-mail(s) |
[email protected]
|
| Organization name |
Peking union medical college
|
| Department |
Institute of medicinal biotechnology
|
| Street address |
1 Tiantan Xili, Dongcheng District, Beijing
|
| City |
Beijing |
| ZIP/Postal code |
100000 |
| Country |
China |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE199508 |
Transcriptome profiling of miRNA and mRNA of the cortex in a rat model of Vascular dementia by RNA-sequencing |
|
| Relations |
| BioSample |
SAMN28861723 |
| SRA |
SRX15592670 |
