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Sample GSM8706918 Query DataSets for GSM8706918
Status Public on Jan 26, 2025
Title HCT cells, DNA-PK KO, with hypoxicstress, rep2
Sample type SRA
 
Source name HCT116 cells
Organism Homo sapiens
Characteristics cell line: HCT116 cells
cell type: human colon cancer
genotype: DNA-PK knockout
treatment: CoCl2 treatment
Treatment protocol Cells were treated with CoCl2 at a final concentration of 200 µM for 12 hours to induce hypoxia. Control cells were treated with the same amount of H2O.
Growth protocol WT and DNA-PK KO HCT116 cells were grown in DMEM-high glucose (Cytiva Hyclone, SH30243.01) medium to approximately 60% confluence.
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted and purified from cells using the RNeasy kit (Qiagen).
RNA was converted into cDNA and sequenced by Omega Bioservices according to previously described protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description Library name: DNA-PK KO HCT cells, hypoxic stress rep2
B5_S60
Data processing Sequenced reads (paired-end) in FASTQ format were trimmed using Trim Galore (version 0.6.6) with Cutadapt (version 3.4) and their quality was assured using FastQC (version 0.11.9).
Quality-assured trimmed reads were then aligned to the reference genome (hg38 assembly) using STAR (version 2.7.9a) with the following parameters: --outSAMtype BAM SortedByCoordinate, --quantMode TranscriptomeSAM, and --outFilterMultimapNmax 1.
The integrity of transcripts was evaluated by means of transcript integrity number (TIN) scores using RseQC (tin.py, version 4.0.0).
Gene expression levels were quantified using StringTie (version 2.1.7b), and differential gene expression analysis was conducted using DESeq2 (version 1.36.0) to identify genes with significant changes between conditions.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample
 
Submission date Jan 02, 2025
Last update date Jan 26, 2025
Contact name Jihye Park
E-mail(s) apjh1998@dankook.ac.kr
Organization name Dankook University
Street address 119 Dan-daero, Dongnam-gu
City Cheonan
ZIP/Postal code 31116
Country South Korea
 
Platform ID GPL20795
Series (1)
GSE285698 DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [RNA-Seq]
Relations
BioSample SAMN46052893
SRA SRX27230297

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

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