|
| Status |
Public on May 03, 2024 |
| Title |
A375_DMSO #_Crt_2 |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma cell line A375
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
treatment: DMSO
|
| Treatment protocol |
cells has been treated with dabrafenib at concetration of 200nM for 48h and with DMSO (0.1%)
|
| Growth protocol |
RPMI 10%FBS, splitting every 48-72h at confluency
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was quantified and mixed at 10ng/µl
Total RNA (250 ng) from each sample was prepared using Small RNA-Seq Library Prep Kit (Lexogen, GmbH), according to manufacturer's instructions
The library product were cleaned-up and concentrated with gel-based purification protocol. This step removes linker-linker artefacts (120 bp) and long library fragments (>200bp) . The sequencing step was performed with NGS technologies using Illumina Novaseq 6000 SP kit (100 cycles) produced by Illumina.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
SmallTranscriptome profile of A375 treated with DMSO (0.1%), biological rep2
|
| Data processing |
We compared the miRNA expression profiles between the A375 and A375-BIR cells in both control (DMSO) and treatment group by using EdgeR package (https://www.bioconductor.org/packages/release/bioc/html/edgeR.html) under software R (version 4.0.2). MiRNAs that have very low counts across all the libraries were re- moved prior to perform normalization by trimmed mean of M values (TMM)
Genome_build: Reads were aligned and assigned to Human ENSEMBLE transcripts and genes (hg38 reference) by using RSEM version 1.2.25 with standard parameters.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
|
| |
|
| Submission date |
Jan 22, 2021 |
| Last update date |
May 03, 2024 |
| Contact name |
Rossella De Cegli |
| E-mail(s) |
decegli@tigem.it
|
| Phone |
08119230692
|
| Organization name |
Tigem
|
| Street address |
Via Campi Flegrei 34
|
| City |
Pozzuoli |
| ZIP/Postal code |
80078 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE165335 |
SmallRNAome profile of melanoma cell lines A375 and A375-BIR (BIR-BRAF INHIBITOR RESISTANT) during dabrafenib treatment |
| GSE165338 |
RNAseq and Small-RNAseq dataset to comprehensively study the miRNA expression profiling of drug-resistant melanoma patients and cell lines |
|
| Relations |
| BioSample |
SAMN17496793 |
| SRA |
SRX9920596 |
