|
| Status |
Public on Jul 20, 2021 |
| Title |
sicntrl_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
FaDu cells (OSCC cell line ATCC)
|
| Organism |
Homo sapiens |
| Characteristics |
experimental condition: si_control
cell line: FaDu
|
| Treatment protocol |
CCNA1 Knock Down was performed using the Lipofectamin RNAiMax transfection reagent (INVITROGEN) according to the manufacturer’s protocol. The siRNA sequence targeting CCNA1 was GAACCUGGCUAAGUACGUA, and the RNA sequence used as Control was the siRNA pGL3 luciferase control (Eurogentec reference SR-CL011-005).
|
| Growth protocol |
FaDu cell line (ATCC- HTB-43) were subcultured in EMEM complete medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extractions were performed from control and CCNA1 knock down FaDu cells in independent triplicates for each condition. RNA was extracted from each sample directly after cell harvesting with TRIZOL, following the manufacturer’s protocol (AMBION). RNA pellets were dissolved in RNAse-free water, and then cleaned up on QIAGEN columns using the RNA Clean Up protocol of RNeasy Mini Kit (QIAGEN), which includes an on column-DNase treatment of 15 minutes. RNA was eluted with 40 µl of RNAse-free water and its concentration measured with Nanodrop.
RNAseq was subcontracted to BGI Tech Solution (Hong Kong). For each sample, 1 µg RNA was used for libraries preparation with LncRNA library(H/M/R) according to the manufacturer’s instructions and sequenced on a DNBSEQ PE100 Eukaryotic Long Non-Coding RNA platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
The sequenced reads were aligned from raw sequence fastq data using STAR v2.5.2b software on UCSC hg38 reference genome.
The aligned reads were normalized using the R bioconductor package DEseq2 (http://bioconductor.org/packages/3.12/bioc/html/DESeq2.html) and then pseudo log2 tranformed using the following formula: log2(norm_count + 1).
Genome_build: hg38
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Apr 05, 2021 |
| Last update date |
Jul 20, 2021 |
| Contact name |
Sophie Rousseaux |
| Organization name |
INSERM-UGA
|
| Department |
IAB
|
| Lab |
U1209
|
| Street address |
Bd de la Chantourne
|
| City |
La Tronche |
| ZIP/Postal code |
38706 |
| Country |
France |
| |
|
| Platform ID |
GPL28038 |
| Series (1) |
| GSE171506 |
The combined detection of Amphiregulin, Cyclin A1 and DDX20/Gemin3 expression predicts aggressive forms of Oral Squamous Cell Carcinoma |
|
| Relations |
| BioSample |
SAMN18620248 |
| SRA |
SRX10514903 |
