|
| Status |
Public on May 01, 2024 |
| Title |
HCC38 IFN-β biol rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HCC38
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC38
genotype: WT
treatment: IFN-Beta
|
| Treatment protocol |
HCC38 and MDA-MB-231 cell lines were treated with with interferon-β (400 IU/mL) for 48 hours.
|
| Growth protocol |
HCC38 and MDA-MB-231 cells were maintained in RPMI-1640 medium and DMEM (1 g/L glucose) respectively. All growth media were supplemented with 10% fetal calf serum (FCS) and penicillin/streptomycin (100 units/mL). Both cell lines were cultured at 37 °C supplied with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini kit (Qiagen).
The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina"
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and BclConvert v4.2.4
Sequence reads were trimmed to remove possible adapter sequences and filtered on low-quality bases using fastp v0.23.2.
The trimmed reads were mapped to the human GRCh38.p13
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v2.0.2.
To enable comparison of gene/transcript expression across all samples outside of the context of differential expression analysis, FPKM and CPM values were calculated with Cufflinks v2.2.1
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
|
| |
|
| Submission date |
Apr 15, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Marcel van Vugt |
| Organization name |
University Medical Center Groningen
|
| Street address |
Hanzeplein 1
|
| City |
Groningen |
| State/province |
Netherlands |
| ZIP/Postal code |
9713 GZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE263947 |
IRF3 drives replication stress signaling and determines sensitivity to genotoxic agents in triple-negative breast cancer cells |
|
| Relations |
| BioSample |
SAMN40971264 |
| SRA |
SRX24329641 |
