|
| Status |
Public on Dec 18, 2019 |
| Title |
e11-1-RNAPII |
| 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
chip antibody: anti-RNA polymerase II (CTD4H8, Millipore, lot 2810725)
|
| 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), 20% 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 |
Lysate was isolated from formaldehyde cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody.
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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 bwa mem.
Duplicate reads and reads mapping to blacklist regions or the mitochondria were removed.
Peak-calling was performed using MACS2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: _peaks.narrowPeak: bed files of macs2 peaks.
|
| |
|
| 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) |
| GSE120812 |
HBO1 is required for the maintenance of leukaemia stem cells [ChIP-seq] |
| GSE120813 |
HBO1 is required for the maintenance of leukaemia stem cells |
|
| Relations |
| BioSample |
SAMN10174405 |
| SRA |
SRX4796160 |
