|
| Status |
Public on Nov 04, 2018 |
| Title |
MOLM13_dBRD9-6d_RNA-Seq_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MOLM13 (AML)
|
| Organism |
Homo sapiens |
| Characteristics |
agent: dBRD9
cell line: MOLM13
|
| Treatment protocol |
MOLM-13 and TTC1240 were treated with (1:10,000) DMSO vehicle control or 250nM dBRD9 to chemically degrade BRD9 for 6 days (MOLM-13) or 7 days (TTC1240) in biological duplicate followed by harvesting of RNA.
|
| Growth protocol |
Malignant rhabdoid tumor cell line TTC1240 were grown in DMEM (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco). MOLM-13 cells were grown in RPMI (Gibco) supplemented with 10% FBS, 1% GlutaMAX (Gibco), and 1% penicillin-streptomycin (Gibco)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was collected from 2 million cells per condition, in biological duplicate, 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 |
MOLM13_dBRD9-6d_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 |
Aug 09, 2018 |
| Last update date |
Nov 04, 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 |
Massachusetts |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE113041 |
A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation [RNA-seq] |
| GSE113042 |
A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation |
|
| Relations |
| BioSample |
SAMN09788756 |
| SRA |
SRX4525869 |
