|
| Status |
Public on Oct 09, 2019 |
| Title |
GC077042_TCGACGTC-CTATTAAG_primary_superficial_sc |
| Sample type |
SRA |
| |
|
| Source name |
mitfa:GFP cell from primary_superficial triple melanoma
|
| Organism |
Danio rerio |
| Characteristics |
genotype: mitfa:BRAFV600E;mitfavc7;p53M214K
tissue: GFP+ cell from primary_superficial triple melanoma
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
FACS sorting of a single GFP+ living cell from primary tumour, SMARTseq2 (Picelli et al 2014)
polyA selection
cDNA - Nextera XT
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NexteraXT library preparation
|
| Data processing |
Sequence quality was checked using FastQC (version 0.11.4). Raw reads were trimmed, using Cutadapt to remove Smart-Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 (Ensembl V92, 20178) including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment-based mode.
|
| |
|
| Submission date |
Sep 05, 2019 |
| Last update date |
Oct 09, 2019 |
| Contact name |
Jana Travnickova |
| E-mail(s) |
jana.travnickova@igmm.ed.ac.uk
|
| Organization name |
MRC Human Genetics Unit & Cancer Research UK EC
|
| Department |
MRC Institute of Genetics and Molecular Medicine
|
| Lab |
Prof. Patton lab
|
| Street address |
Crewe Road South
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE136900 |
MITF-low melanoma subtype models in zebrafish reveal transcriptional sub-clusters and MITF-independent residual disease |
|
| Relations |
| BioSample |
SAMN12698120 |
| SRA |
SRX6804386 |
