|
| Status |
Public on May 21, 2019 |
| Title |
Resistant Input for Click-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: IBET
|
| 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 |
genomic DNA |
| Extraction protocol |
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then chem-precipitation was performed with pre-clicked JQ1 biotin conjugated beads
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Library strategy: Click-seq
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
Supplementary_files_format_and_content: bed files of macs2 peaks
|
| |
|
| 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) |
| GSE110897 |
Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia [Click-seq] |
| GSE110901 |
Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia |
|
| Relations |
| BioSample |
SAMN08569883 |
| SRA |
SRX3729382 |
