|
| Status |
Public on Apr 04, 2020 |
| Title |
Mel202WT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mel202 uveal melanoma, cell line
|
| Organism |
Homo sapiens |
| Characteristics |
agent: Uninduced
cell line: Mel202
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TriZol and the RNeasy Mini RNA isolation kit with RNAase-Free DNase treatment (Qiagen).
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA prep kit with Ribo-Zero Gold to remove cytoplasmic and mitochondrial rRNA according to the manufacturer's recommendation (Illumina, Inc.).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw RNA-Seq FASTQ files were assessed for quality using FastQC
Sequenced reads were aligned to the human genome (hg19) using STAR with the following settings --runThreadN 16 --genomeSAindexNbases 12 --genomeSAsparseD 2 --genomeDir /nethome/mfield/ref_files/ENSEMBL/STAR_genomedirectory --readFilesIn /scratch/projects/hlab/newRNAseq/F46.fastq.gz --readFilesCommand zcat --outFileNamePrefix /scratch/projects/hlab/newRNAseq/STAR/F46 --outSAMtype BAM SortedByCoordinate --chimSegmentMin 12 --quantMode GeneCounts --alignIntronMax 200000 --alignMatesGapMax 200000 --alignSJDBoverhangMin 10 --chimJunctionOverhangMin 12 --twopassMode Basic --twopass1readsN -1
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file with gene count file output from STAR
|
| |
|
| Submission date |
Apr 26, 2019 |
| Last update date |
Apr 05, 2020 |
| Contact name |
Matthew G. Field |
| Organization name |
University of Miami
|
| Street address |
1501 NW 10th Avenue
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE130356 |
BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas [RNA-Seq] |
| GSE130357 |
BAP1 loss triggers DNA methylomic repatterning in highly aggressive Class 2 uveal melanomas |
|
| Relations |
| BioSample |
SAMN11514562 |
| SRA |
SRX5741433 |
