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Sample GSM8278872 Query DataSets for GSM8278872
Status Public on Jun 17, 2024
Title Left ventricle, WKY, rep2
Sample type SRA
 
Source name Left ventricle
Organism Rattus norvegicus
Characteristics tissue: Left ventricle
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 SAMN41017833
SRA SRX24309905

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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