|
| Status |
Public on Dec 01, 2023 |
| Title |
HepG2_24h_1 |
| Sample type |
SRA |
| |
|
| Source name |
liver tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: liver tumor
cell line: HepG2
cell type: Hepatoblastoma
genotype: p53 wild type
treatment: Control
|
| Treatment protocol |
Sorafenib was added at the concentration of 10 µM at 24 h hours after transfection, and lysates were obtained after 24 hours after treatment. Control cells were treated in parallel with dimethyl sulfoxide (DMSO), vehicle in wich Sorafenib was dissolved.
|
| Growth protocol |
Cells were cultured in minimal essential medium (MEM) with Earle's balanced salts with L-glutamine suplemented with 10% fetal bovine serum, 1% sodium pyruvate, 1% non-essential amino acids and penicillin-streptomycin solution; cells were grown in culture flasks at 37 ºC in a humidified incubator with 5% CO2. Cells were plated at 50.000 cells/cm2 and transfected with Lipofectamine RNAimax after 24h with miR-200c-3p inhibitor, miR-222-5p mimic, miR-512-3p mimic and transfection controls. Media was changed 6 hours later
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a miRNeasy mini kit with DNase treatment according to the manufacturer’s instructions(QIAGEN, Germany).
Libraries were prepared using total RNA lysates. Total RNA concentration and quality of the RNA were assessed with Qubit (Qubit™ DNA HS assay) and TapeStation 4150 with the RNA ScreenTape Assay (Agilent Technologies Genomics, USA), respectively. RNA Integrity Number (RIN) values were assessed. Libraries were constructed from 100 ng of RNA with the Illumina Stranded TOTAL RNA prep Ligation with RIBO-ZERO PLUS. Libraries were amplified, purified and subjected to quality control with High Sensitivity DNA Qubit® Assay and High Sensitivity D100 ScreenTape Assay (average size 260-280 bp). Samples were then pooled together at 2.4 nM, diluted at 1.2 nM (PhiX included) and sequenced in NovaSEq6000 S1 instrument from Illumina (2x75 cycles)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecall, trimming and demultiplexing were carried out with DRAGEN FASTQ Generation software and Illumina FastQ generation tool
Secondary analysis, concerning alignment, mapping and differential expression analysis, was carried out using Illumina BaseSpace Apps "RNAseq Aligment" and "DESeq2"
Reads were mapped to the human genome version GRCh38 using STAR Aligner
Differential expression analysis was performed using the DESeq2 method
Assembly: GRCh38
Supplementary files format and content: 2 Matrix tables with raw and normalized gene counts for every gene and every sample
Supplementary files format and content: Text files with normalized gene counts per sample
|
| |
|
| Submission date |
Feb 17, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Patricia de la Cruz-Ojeda |
| Organization name |
Institute of Biomedicine of Seville
|
| Lab |
209
|
| Street address |
Avda. Manuel Siurot s/n
|
| City |
Sevilla |
| ZIP/Postal code |
41011 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE225537 |
Total RNAseq of HepG2 cells treated with Sorafenib |
|
| Relations |
| BioSample |
SAMN33339287 |
| SRA |
SRX19402521 |
