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Sample GSM5726817 Query DataSets for GSM5726817
Status Public on Dec 01, 2023
Title Pulsatilla Chinensis rep2
Sample type SRA
Source name Pulsatilla Chinensis treated
Organism Homo sapiens
Characteristics cell line: HepG2
cell type: hepatocellular carcinoma cell line
sample type: experimental group
treatment: 125ng/mL of PC for 24 h
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 Homo sapiens(GRCh38) whole genome using HISAT2(v2.1.0).
Sequence reads aligned to the human 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 GPL24676
Series (2)
GSE190628 RNA-Sequencing of HepG2 cells treated with Chinese herbal medicine Pulsatilla Chinensis
GSE190631 RNA-Sequencing of HepG2 cells and rats treated with Chinese herbal medicine Pulsatilla Chinensis
BioSample SAMN23848298
SRA SRX13374660

Supplementary file Size Download File type/resource
GSM5726817_PC_2.txt.gz 306.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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