|
Status |
Public on Mar 11, 2019 |
Title |
Bin67_K785R_RNA-Seq_Rep1 |
Sample type |
SRA |
|
|
Source name |
BIN-67 (SCCOHT)
|
Organism |
Homo sapiens |
Characteristics |
lentivirus: K785R 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_K785R_RNA-Seq_Rep1
|
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 |
SAMN09689617 |
SRA |
SRX4404497 |