|
| Status |
Public on Nov 03, 2016 |
| Title |
LM-MEL-33 |
| Sample type |
SRA |
| |
|
| Source name |
melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: melanoma
epithelial-like or mesenchymal-like: mesenchymal-like
braf mutation: V600E/K
tumour site: lymph node
|
| Growth protocol |
Cell lines were derived from melanoma tumours of our clinical unit. Single cell suspensions were generated from biopsy samples collected fresh and subjected to manual dissociation followed by collagenase/DNAse digestion (4-12 hours). Cell suspensions were plated in RPMI1640 media supplemented with 1% penicillin/streptomycin, 1% GlutaMAX and 10% fetal bovine serum until establishment of viable cell lines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted from cell pellets lysates using the Qiagen miRNeasy Mini Kit (Cat No 217004) and RNA quality confirmed by bioanalyzer prior to library preparation
small RNA libraries were prepared according to standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
For each sample, raw read data (fastq format) was concatenated using the UNIX command line and subsequently collapsed to provide sums of reads for any sequence detected more than once, using the FASTX-Toolkit (v0.0.13) command-line tool "FASTX-collapser" using default settings and the -Q33 switch
Collapsed raw read data in fasta format was submitted to the miRanalyzer webserver pipeline, accessed at http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php and underwent genome alignment (hg18 build), microRNA quantification and classification as mature, star, hairpin, or precursor forms, with reference to miRBase v18.
Read count data for all mature microRNA sequences was extracted and compiled into a data matrix for all samples in R.
Genome_build: hg18
Supplementary_files_format_and_content: raw and RPKM count data for all mature microRNA sequences identified in at least one sample across all 57 melanoma cell lines
|
| |
|
| Submission date |
Nov 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Miles Andrews |
| E-mail(s) |
[email protected]
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Surgical Oncology
|
| Lab |
Wargo Lab
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE89438 |
Identification of functional interactions through integration and systems analysis of matched gene and microRNA expression data across the Ludwig-Melbourne Melanoma (LM-MEL) Cell Line Panel |
|
| Relations |
| BioSample |
SAMN05967952 |
| SRA |
SRX2320806 |
