|
| Status |
Public on Dec 18, 2019 |
| Title |
DMSO.D4.R2 |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF9 I-BET sensitive cells
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
cell type: haematopoietic progenitors
condition: I-BET sensitive
|
| Treatment protocol |
4x10^6 cells were transduced with shRNA pool at multiplicity of infection of 0.3. Following 30 hours of transduction, hairpin positive cells were selected with puromycin.
|
| 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 |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated with DNeasy Blood & Tissue Kit (Qiagen).
shRNA sequences were amplified by PCR with primers.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Pooled shRNA screen
processed data file: Pool1RawCounts.csv
|
| Data processing |
Illumina bcl2fastq v2 software was used for basecalling.
Reads were demultiplexed using a custom in-house script.
Reads were aligned and analysed using edgeR from Bioconductor in R.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Pool1RawCounts.csv: Comma-separated text file of raw counts.
Supplementary_files_format_and_content: Pool1revcompbarcodes.txt: Tab-delimited text file containing the barcodes for each sample in the pool.
Supplementary_files_format_and_content: Pool1revcompshRNA.txt: Tab-delimited text file containing the sequences of each shRNA hairpin in the pool.
|
| |
|
| Submission date |
Oct 18, 2019 |
| Last update date |
Dec 18, 2019 |
| Contact name |
Mark Dawson |
| E-mail(s) |
[email protected]
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan St
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE120813 |
HBO1 is required for the maintenance of leukaemia stem cells |
| GSE139118 |
HBO1 is required for the maintenance of leukaemia stem cells [shRNA screen] |
|
| Relations |
| BioSample |
SAMN13060905 |
| SRA |
SRX7024057 |
