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Sample GSM5726823 Query DataSets for GSM5726823
Status Public on Dec 01, 2023
Title ND rep1
Sample type SRA
Source name normal diet treated
Organism Rattus norvegicus
Characteristics tissue: Liver
sample type: control group
treatment: normal diet treated
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions´╝îIllumina TruSeq RNA Sample was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Demultiplexing and basecalling performed using CASAVA version 1.8.2.
QC was performed on the FASTQ files using FastQC(v0.11.5) software.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rat(Rnor_6.0) whole genome using HISAT2(v2.1.0).
Sequence reads aligned to the rat genome were imported into StringTie(v1.3.3b) for sequence read counting.
Sequence reads mapped to different isoforms of individual genes were pooled together, and then were input into the DESeq2(v1.28.0) differential expression analysis program to normalize and determine expression levels and differentially expressed genes.
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each gene per sample
Submission date Dec 10, 2021
Last update date Dec 01, 2023
Contact name ruijun wang
Phone 18518157361
Organization name Tsinghua university
Street address college of life science
City beijing
ZIP/Postal code 102206
Country China
Platform ID GPL25947
Series (2)
GSE190630 RNA-Sequencing of rats treated with Chinese herbal medicine Pulsatilla Chinensis
GSE190631 RNA-Sequencing of HepG2 cells and rats treated with Chinese herbal medicine Pulsatilla Chinensis
BioSample SAMN23848739
SRA SRX13374679

Supplementary file Size Download File type/resource
GSM5726823_ND_1.txt.gz 273.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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