|
| Status |
Public on Jan 18, 2018 |
| Title |
A375 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: BRAF V600E
passages: 5-50
treatment: non treated
|
| Treatment protocol |
Vemurafenib-resistant A375 cells were derived from parental A375 cells by treatment with sequential increases of vemurafenib (Selleckchem, Houston, TX) concentrations, from 10 nM to 1.3 μM, and were finally maintained as an uncloned resistant cell population in complete medium with 1.3 μM of VMF.
|
| Growth protocol |
Melanoma cell lines were cultured in DMEM medium supplemented with 10% fetal bovine serum (Gibco, Paisley, UK)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mirVana miRNA Isolation kit (Thermo Fisher Scientific, Waltham, MA)
RNA libraries were prepared for sequencing using standard Illumina protocols for small RNAseq
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Non treated Parental A375 melanoma cells
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using cutadapt version 1.7.1.
Trimmed reads were mapped to miRbase 21 using bowtie v1.0.0 with parameters -q --phred33-quals -v 0 --tryhard -k 1 --best --norc
Reads were assigned to microRNA ids and raw counts were produced
Normalized counts were generated with DESeq2 R package
Differential miRNA expression was determined with DESeq2 pipeline (Wald test fit type parametric)
Genome_build: miRbase 21
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample and *norm_DESeq.csv files include normalized counts by size factors
|
| |
|
| Submission date |
Dec 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Marta Diaz Martinez |
| Organization name |
Centro de Investigaciones Biológicas
|
| Lab |
Chemokines and cell migration
|
| Street address |
Ramiro de Maeztu, 9
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE107576 |
miR-204-5p and miR-211-5p contribute to BRAF inhibitor resistance in melanoma |
|
| Relations |
| BioSample |
SAMN08117872 |
| SRA |
SRX3436251 |
