|
| Status |
Public on Oct 05, 2022 |
| Title |
MP41_miRNA-16_12h |
| Sample type |
SRA |
| |
|
| Source name |
uveal melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: mimic 16
|
| Treatment protocol |
All siRNAs and synthetic miRNAs were transfected at 66nM using Lipofectamine RNAiMAX (ThermoFisher Scientific) according to manufacturer’s instructions. For RNA and proteins analysis, 250,000 cells were seeded in 6-well plates.
|
| Growth protocol |
MP41 cell line were maintained in RPMI-1640 medium supplemented with 20% Fetal Bovine Serum (FBS) and 1% Penicillin-Streptomycin antibiotics
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from cell samples using NucleoSpin RNA Plus kit (Macherey-Nagel) and quantified using a NanoDrop 1000 Spectrophotometer (ThermoFisher Scientific).
cDNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
(i) Reads quality control using fastQC and Fastq-scren
(ii) mapping with STAR_2.4.0a versus hg38 following ENCODE RNA-seq options
(iii) features quantification using featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -C" options using Ensembl GRCh38.76 release.
Genome_build: hg38
Supplementary_files_format_and_content: Normalized_Data.txt
|
| |
|
| Submission date |
Jul 19, 2021 |
| Last update date |
Oct 05, 2022 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
|
| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
|
| Street address |
660 route des lucioles
|
| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE180399 |
Oncogenic role of the non-canonical base-pairing between miRNAs/mRNAs in uveal melanoma. |
|
| Relations |
| BioSample |
SAMN20307368 |
| SRA |
SRX11500215 |
