|
| Status |
Public on Aug 09, 2023 |
| Title |
HEPG2 cells, Treatment 3 |
| Sample type |
SRA |
| |
|
| Source name |
HEPG2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEPG2
cell type: Liver hepatocellular carcinoma cells
genotype: WT
treatment: Treatment with microalgea extract at IC50 concentration
time: 24 hrs
|
| Treatment protocol |
3x10^5 treated Ls174 and HepG2 cells were cultured with 0.7 mg/ml extract from Hypnea musciformis for 24 hr
|
| Growth protocol |
Ls174 and HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol (MRC). 1 ug of total RNA was used for the construction of sequencing libraries.
3’ RNA libraries for RNA-seq were prepared using the 3’mRNA Quant Library Prep kit protocol of Ion Torrent following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
HISAT2-BOWTIE2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to GRCh37/hg19 using hisat2 (parameters -un, --add-chrname). Hisat2 unaligned reads were mapped with BOWTIE2 (parameters --local –very-sensitive-local). Hisat2 and Bowtie2 aligned reads were merged.
Read count extraction and normalization were performed using the metaseqR2 Bioconductor package
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Mar 30, 2023 |
| Last update date |
Aug 09, 2023 |
| Contact name |
Antonis Giakountis |
| Organization name |
University of Thessaly
|
| Department |
Biochemistry and Biotechnology
|
| Street address |
Biopolis-Mezourlo
|
| City |
Larissa |
| ZIP/Postal code |
41500 |
| Country |
Greece |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE228578 |
Transcriptomics and proteomics analyses reveal the anti-cancer properties of extract from Hypnea musciformis macroalgea in liver and intestinal cancer cells |
|
| Relations |
| BioSample |
SAMN33988206 |
| SRA |
SRX19821214 |
