|
| Status |
Public on Dec 29, 2021 |
| Title |
M238R.07 |
| Sample type |
SRA |
| |
|
| Source name |
M238R melanoma cells resistant to the BRAF inhibitor Vemurafenib
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: M238R
cell type: human melanoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sequencing libraries were prepared with the Oxford Nanopore LSK-109 library preparation kit (SQK-PCB109 kit)
Sequence using Ofxord Nanopore PromethION (flowcell_id PAE18991),
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
PromethION |
| |
|
| Description |
M238R melanoma cells resistant to the BRAF inhibitor Vemurafenib
|
| Data processing |
MinKNOW 4.0.5B software used for primary data acquisition, basecalling using Guppy v4.0.11
Sequenced raw reads were then processed following the FLAIR workflow (A.D. Tang et al., Nat. Commun. 11,1438 2020). In short, reads were aligned to hg38 with minimap2 (version 2.17-r941). Misaligned splice sites were corrected according to the GENCODE v.35 annotations. High confidence isoforms were defined after grouping corrected reads of all samples sharing same unique splice junctions. Selected isoforms were quantified using minimap2 in each sample
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files containing the matrix of isoforms abundance in both samples
|
| |
|
| Submission date |
Apr 12, 2021 |
| Last update date |
Dec 29, 2021 |
| 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 |
GPL26167 |
| Series (2) |
| GSE171882 |
RNA-Seq analysis (long-reads) of human parental M238P and BRAF inhibitors-resistant M238R melanoma cells |
| GSE171883 |
Blockade of the pro-fibrotic reaction mediated by the miR-143/-145 cluster enhances the responses to targeted therapy in melanoma |
|
| Relations |
| BioSample |
SAMN18714204 |
| SRA |
SRX10578990 |
