|
| Status |
Public on Mar 11, 2019 |
| Title |
Bin67_SMARCA4_RNA-Seq_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
BIN-67 (SCCOHT)
|
| Organism |
Homo sapiens |
| Characteristics |
lentivirus: SMARCA4
cell line: BIN-67
|
| Treatment protocol |
Virus was prepared using co-transfection of lentiviral packaging vectors along with SMARCA4 WT, T910M, K785R, and control in a pLEX307 vector backbone. Concentrated virus was added to 15 cm plates of BIN-67 cells at 70% confluency and selected for 2 days using puromycin. Two days later, cells were harvested for RNA-seq.
|
| Growth protocol |
BIN-67 cell lines were grown in custom media (20% FBS, 40% DMEM, 40% DMEM/Ham’s F12). SCCOHT-1 cell lines were grown in RPMI supplemented with 10% FBS. All media was supplemented with pen/strep.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
One million cells of each condition were harvested using Qiagen RNeasy kit and 1 ug was DNase treated and used in Illumina TruSeq Stranded mRNA library prep kit
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 |
Bin67_SMARCA4_RNA-Seq_Rep2
|
| Data processing |
Basecalls were performed using bcl2fastq v2.19.1 for NextSeq output.
RNA-seq reads were aligned to UCSC hg19 using STAR version 2.5.2a Only uniquely mapping reads with at most two mismatches were retained.
RNA read counts were calculated using GFOLD
Genome_build: hg19
Supplementary_files_format_and_content: read count files for gene expression created using GFOLD
|
| |
|
| Submission date |
Jul 18, 2018 |
| Last update date |
Mar 11, 2019 |
| 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 |
Massachusetts |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE117311 |
The mSWI/SNF ATPase module mediates subcomplex identity and non-catalytic targeting in SCCOHT [RNA-seq] |
| GSE117735 |
The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity-independent genomic targeting |
|
| Relations |
| BioSample |
SAMN09689628 |
| SRA |
SRX4404490 |
