|
| Status |
Public on Apr 18, 2018 |
| Title |
3842_4_A375R_drug_withdrawal |
| Sample type |
SRA |
| |
|
| Source name |
A375R cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: skin cancer
cell line: BRAF mutant melanoma cell line A375R
treatment: drug withdrawal
|
| Treatment protocol |
In vitro: A375, A375R, A375DR cells were treated with 1µM Vorinostat. Patient samples, Patients were treated with Vorinostat (a safe single oral daily dose of 360 mg)
|
| Growth protocol |
A375 parental, cells grow in DMEM-based medium supplemented with 10% FBS, 1% penicillin/streptomycin and 2 mM L-glutamine. A549 cell grow in RPMI-based medium supplemented with 10% FBS, 1% penicillin/streptomycin and 2 mM L-glutamine. A375R were cultured in the same culture condition plus 2µM vemurafenib. A375DR cells were cultured in the same culture condition plus 0.5µM Dabrafenib and 10nM Trametinib
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
A375, A375R and A375DR RNA was isolated using TRIZOL, patient biopisy RNA isolation kit from qiagen
Stranded RNA libraries were prepared for sequencing according to Illumina instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
polyA+ stranded RNA Library prep from cells
|
| Data processing |
The reads were sequenced using a stranded protocol and aligned against the human genome, build 38, using Tophat 2.1 with bowtie 1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count. Genes that have no expression across all samples are removed from the dataset.
To aviod noise fold change caused by low reads. The reads counts from In vitro A375 A375R and A375DR were filtered greater than 50
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples
|
| |
|
| Submission date |
Feb 21, 2018 |
| Last update date |
Apr 18, 2018 |
| Contact name |
Liqin Wang |
| E-mail(s) |
l.wang@nki.nl
|
| Phone |
0031205121958
|
| Organization name |
NKI-AVL
|
| Department |
B7
|
| Lab |
Bernards
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE110948 |
RNA Seq data: A375, A375R, A375DR vorinostat treated, and biopy samples from patients pre- and post- treated with Vorinostat |
| GSE111141 |
An acquired vulnerability of drug resistant melanoma with therapeutic potential |
|
| Relations |
| BioSample |
SAMN08578902 |
| SRA |
SRX3730201 |
