|
| Status |
Public on Apr 02, 2020 |
| Title |
Control1 |
| Sample type |
SRA |
| |
|
| Source name |
Basilar artery smooth muscle cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Spraque-Dawley
tissue: Brain basilar arteries
weight: 180-200g
model: N/A
|
| Growth protocol |
All the animals were fed under free food and water. The high-salt diet comprised rat chow supplied for control group rat and additional 4% (w/w) sodium chloride (NaCl). When the systolic blood pressure levels were determined by tail-cuff method and significantly increased above 30 mmHg in the rats eating the high-salt diet for 4 weeks .
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
All these rats were sacrificed by continuously inhaling carbon dioxide. The rats’ brains were isolated and put in the Kreb’s solution. Brain basilar arteries were isolated, and then unnecessary connective tissues were eliminated by using anatomical microscope. By mechanically removed using wires repeatedly, the endothelial cells were denuded.
All the remain basilar artery smooth muscle cells of each single rat were collected, and then messenger RNAs extractions were performed using Poly A selection of Illumina TruSeq RNA sample preparation protocol to establish the RNA sample libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
C1
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
The RNA sequencing (RNA-Seq) Fastq raw data were pruned using Trimmomatic to remove adaptors and lower mass reads. The quality of clean data was assessed using FastQC software. The quality-approved data were mapped to the reference genome of the rat (National Center for Biotechnology Information [NCBI] genome assembly, version Rnor_6.0) using HISAT2 (v2.0.13) and annotated with the annotation file (.gtf) NCBI Rnor_6.0.
The RNA-Seq quantification software Kallisto was used to obtain a count of known messenger RNAs (mRNAs) to compare the differences in transcript expression. Using the edgeR package software (http://bioconductor.org/packages/2.4/bioc/html/edgeR.html), the differences in the number of reads among samples were analyzed.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample
|
| |
|
| Submission date |
Apr 01, 2020 |
| Last update date |
Apr 03, 2020 |
| Contact name |
Lesha Zhang |
| E-mail(s) |
zls_simm@126.com
|
| Phone |
+8617756077697
|
| Organization name |
Anhui Medical University
|
| Department |
Physiology
|
| Street address |
81 Meishan road
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230001 |
| Country |
China |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE147945 |
High-throughput RNA sequencing of basilar artery smooth muscle cells in wild type and high-salt diet induced hypertension rats |
|
| Relations |
| BioSample |
SAMN14521641 |
| SRA |
SRX8044324 |
