|
| Status |
Public on May 31, 2018 |
| Title |
Aska naive 1 |
| Sample type |
SRA |
| |
|
| Source name |
Aska (SS)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Aska (SS)
|
| Treatment protocol |
Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). The cells were harvested following 48-hour exposure to the lenti-virus and either 1 day (3 days post-infection) or 5 days (7 days post-infection) of selection with 2 μg/ml of puromycin.
|
| Growth protocol |
All cell lines were cultured in DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10-20% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco) and 1% Penicillin-Streptomycin (Gibco).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
All RNA was produced using the RNeasy Mini Kit (Qiagen).
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Aska naive 1 RNA-seq
|
| Data processing |
RNA-seq reads were mapped to the human reference genome (hg19) using STAR(Dobin et al., 2013) version 2.3.1 with default parameters.
RPKM values for biological duplicate RNA-seq samples were generated using GFold(Feng et al., 2012) version 1.1.0.
Genome_build: hg19
Supplementary_files_format_and_content: read_cnt
Supplementary_files_format_and_content: GeneSymbol GeneName Read Count Gene Exon Length RPKM
|
| |
|
| Submission date |
Dec 13, 2017 |
| Last update date |
May 31, 2018 |
| Contact name |
Cigall Kadoch |
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Kadoch Lab
|
| Street address |
450 Brookline Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE108026 |
The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma [RNA-Seq Cell] |
| GSE108028 |
The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma |
|
| Relations |
| BioSample |
SAMN08172098 |
| SRA |
SRX3468059 |
