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Status |
Public on Jan 26, 2025 |
Title |
HCT cells, DNA-PK KO, with hypoxicstress, rep2 |
Sample type |
SRA |
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|
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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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|
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
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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 |