|
| Status |
Public on Jun 24, 2021 |
| Title |
KT5_DM_1: SUDHL4 IKZF1 KO DMSO |
| Sample type |
SRA |
| |
|
| Source name |
Diffuse large B-cell lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUDHL4 IKZF1 KO
cell type: Diffuse large B-cell lymphoma
treatment: DMSO
|
| Treatment protocol |
The following model systems were used for RNA-seq: 1) RL cells treated with DMSO, 10μM lenalidomide, 5μM tazemetostat or combination; 2) SUDHL4 cells treated with DMSO, 10μM lenalidomide, 5μM tazemetostat or combination; and 3) SUDHL4 cells with either IKZF1 knockout or LacZ gRNA control treated with DMSO or 5μM tazemetostat. Two technical replicates of all samples and conditions were prepared. Cells were incubated with drug treatments for 6 days.
|
| Growth protocol |
SUDHL4 parental and engineered cell lines were grown at 37°C with 5% CO2 in RPMI 1640 supplemented with 2mM L-glutamine and 20% FBS. RL cells were cultured similarly in medium with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen)
Illumina TruSeq Stranded mRNA Library Prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Raw reads were mapped to hg19 using the STAR 2.7.3a two pass mode.
Gene counts were generated using "quantMode GeneCounts" from within STAR.
Genome_build: hg19
|
| |
|
| Submission date |
Jun 02, 2020 |
| Last update date |
Jun 24, 2021 |
| Contact name |
Robert Kridel |
| Organization name |
Princess Margaret Cancer Centre
|
| Street address |
101 College Street, Rm 12-311
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE151607 |
Combined inhibition of EZH2 and degradation of Ikaros has synergistic effects in germinal center B-cell diffuse large B-cell lymphoma [RNA-seq] |
| GSE152069 |
Combined inhibition of EZH2 and degradation of Ikaros has synergistic effects in germinal center B-cell diffuse large B-cell lymphoma |
|
| Relations |
| BioSample |
SAMN15080930 |
| SRA |
SRX8452867 |
