|
Status |
Public on Jun 30, 2020 |
Title |
Smug1-KO rep2 |
Sample type |
SRA |
|
|
Source name |
HepG2
|
Organism |
Homo sapiens |
Characteristics |
genotype: Smug1 knock-out
|
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 |
SAMN14089621 |
SRA |
SRX7714577 |