|
| Status |
Public on Jun 17, 2024 |
| Title |
Superior cervical ganglion, SHR, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Superior cervical ganglion
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Superior cervical ganglion
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent (Thermo Fisher Scientific). 200 ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using KAPA RNA HyperPrep Kit following manufacturer's protocols on the BGISEQ-500 sequencing platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com)
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseqor PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001)
Assembly: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
May 17, 2024 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Chaohong Li |
| E-mail(s) |
lichaohong@stu.cqmu.edu.cn, sxycjslch@163.com
|
| Organization name |
Chongqing Medical University
|
| Street address |
Yuzhong Road
|
| City |
Chongqing |
| ZIP/Postal code |
400000 |
| Country |
China |
| |
|
| Platform ID |
GPL30103 |
| Series (1) |
| GSE267794 |
Transcriptome landscape of the adrenal gland and superior cervical ganglion from hypertension-induced left ventricular hypertrophy rat model |
|
| Relations |
| BioSample |
SAMN41017854 |
| SRA |
SRX24309919 |
