|
| Status |
Public on May 21, 2019 |
| Title |
Resistant DMSO Rep 1 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF9 I-BET resistant cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: haematopoietic progenitors
condition: I-BET Resistant
strain: C57BL/6
|
| Treatment protocol |
I-BET151 was used at a final concentration of 1000nM. LSD1i was used at a final concentration of 500nM.
|
| Growth protocol |
Cell lines were grown in RPMI-1640 supplemented with mouse IL-3 (10ng/ml), 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37°C). MLL-AF9 I-BET resistant cells were cultured with constant I-BET treatment (1000nM, 0.1% DMSO), while MLL-AF9 I-BET sensitive cells were cultured with constant DMSO treatment (0.1%).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy kit
Libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep kit (Lexigen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using tophat2 and bowtie2
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
|
| |
|
| Submission date |
Feb 20, 2018 |
| Last update date |
May 21, 2019 |
| Contact name |
Mark Dawson |
| E-mail(s) |
mark.dawson@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE110899 |
Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [RNA-seq] |
| GSE110901 |
Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia |
|
| Relations |
| BioSample |
SAMN08569865 |
| SRA |
SRX3729253 |
