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Sample GSM4308521 Query DataSets for GSM4308521
Status Public on Jun 30, 2020
Title Wild-type rep1
Sample type SRA
 
Source name HepG2
Organism Homo sapiens
Characteristics genotype: wild type
Treatment protocol The cells were not treated with chemicals in both control and KO groups.
Growth protocol We established stable KO cell line for Smug1 gene. Smug1-KO HepG2 cells were cultured with DMEM with 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent and mRNA was extracted by mRNA pull-down using poly-A tagged bead.
RNA libraries were prepared for sequencing using standard Truseq RNA Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava software used for basecalling.
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using systempipeR.
Alignment to GRCh38.97 whole genome with Rsubread 1.34.6 and read feature counting with DESeq2.
Normalized by voom function from limma and edgeR.
FPKM were calculated using a fpkm function from DESeq2 and differential gene expression by edgeR.
Genome_build: GRCh38.97
Supplementary_files_format_and_content: txt files include raw counts, normalized counts(FPKM)
 
Submission date Feb 12, 2020
Last update date Jun 30, 2020
Contact name Jung-Woong Kim
E-mail(s) jungkim@cau.ac.kr
Organization name Chung-Ang University
Department Life Science
Lab Genome Dynamics Lab
Street address 84 Heuksuk-ro Dongjak-ku
City Seoul
ZIP/Postal code 06974
Country South Korea
 
Platform ID GPL16791
Series (1)
GSE145210 Transcriptome network analysis of Smug1 knock-out cells by using CRISPR/Cas9 system
Relations
BioSample SAMN14089624
SRA SRX7714574

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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