|
| Status |
Public on Dec 18, 2019 |
| Title |
e11_1_rep_3 |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF9 I-BET resistant cells
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
cell type: haematopoietic progenitors
condition: I-BET Resistant
treatment: e11_1_HBO1_sgRNA
|
| Treatment protocol |
Cell lines were removed from IBET and transduced with sgRNA targeting HBO1/ROSA26. Following 24 hours of transduction, sgRNA positive cells were selected with puromycin (5ug/ml) for a further 72 hours.
|
| Growth protocol |
Cell lines were grown in RPMI-1640 supplemented with mouse IL-3 (10ng/ml), 10% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax (2nM), 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).
|
| Extracted molecule |
total 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 |
| |
|
| Description |
e11.1_3
PolyA RNA
processed data file: CPManno.txt
|
| Data processing |
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using HISAT2.
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CPManno.txt: Tab-delimited text file includes CPM values for each Sample.
|
| |
|
| Submission date |
Oct 03, 2018 |
| Last update date |
Dec 18, 2019 |
| Contact name |
Mark Dawson |
| E-mail(s) |
mark.dawson@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan St
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE120811 |
HBO1 is required for the maintenance of leukaemia stem cells [RNA-seq] |
| GSE120813 |
HBO1 is required for the maintenance of leukaemia stem cells |
|
| Relations |
| BioSample |
SAMN10174393 |
| SRA |
SRX4796157 |
