Reagents and tools table
| Reagent/resource | Reference or source | Identifier or catalogue number |
|---|---|---|
| Experimental models | ||
| MCF7 cell line | Garvan Institute | Authenticated independently by analysis of microsatellite profiles in PCR amplified DNA extracted from the cells; short tandem repeat (STR) validation was performed using references from ATCC/DSMZ |
| HEK293T cell line | Garvan Institute | Authenticated independently by analysis of microsatellite profiles in PCR amplified DNA extracted from the cells; short tandem repeat (STR) validation was performed using references from ATCC/DSMZ |
| U2OS cell line | CellBank Australia | 92022711 |
| Recombinant DNA | ||
| pET12a | Garvan Institute | |
| Antibodies | ||
| iMab scFv-Hisx6-FLAGx3 | Garvan Institute | |
| Oligonucleotides and other sequence-based reagents | ||
| DNA oligonucleotides | Integrated DNA Technologies | Table EV1 |
| Chemicals, enzymes and other reagents | ||
| DPBS | ThermoFisher | 14190144 |
| Dulbecco’s Modified Eagle Medium (DMEM, high glucose, GlutaMAX™ Supplement) | ThermoFisher | 10566016 |
| SuperBlock™ Blocking Buffer | ThermoFisher | 37515 |
| Software | ||
| MEME v 5.3.3 | Bailey et al, 2009 | |
| R version 4.0.4 | R Core Team, 2021 | |
| bedtools | Quinlan and Hall, 2010 | |
| deepTools version 3.5.0 | Ramírez et al, 2016 | |
| Cutadapt version 3.5 | Kechin et al, 2017 | |
| FastQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | Andrews, 2010 | |
| bowtie2 Version 2.4.5 | Langmead et al, 2019 | |
| Samtools Version 1.10 | Danecek et al, 2021 | |
| macs2 Version 2.2.7.1 | Zhang et al, 2008 | |
| bedops Version 2.4.39 | Neph et al, 2012 | |
| picard Version 2.25.6 | http://broadinstitute.github.io/picard/ | |
| HOMER Version 4.11.1 | Heinz et al, 2010 | |
| Prism version 9 | GraphPad Software, Boston, Massachusetts USA, www.graphpad.com | |
| BLItz Pro software version 1.3. | ForteBio | |
| Other | ||
| Genomic DNA from cells was harvested using an AllPrep DNA/RNA/miRNA Universal Kit | QIAGEN | 80224 |
| Amicon Ultra-0.5 Centrifugal Filter Unit | Millipore | UFC501096 |
| ssDNA/RNA Clean & Concentrator kit | Zymo | D7011 |
| AFA Fibre Pre-Slit Snap-Cap microtubes | Covaris | 520045 |
| M220 Focused-ultrasonicator, Covaris instrument | Covaris | |
| 96-well MaxiSorp plate | Thermo Scientific | 442404 |
| No-shearing IDT xGEN cfDNA & FFPE DNA | Integrated DNA Technologies | |
| 4200 TapeStation instrument | Agilent Technologies | |
| D1000 ScreenTapes | Agilent Technologies | 5067-5582 |
| NovaSeq 6000 SP reagent kit | Illumina | 20028312 |
| Illumina NovaSeq 6000 | Illumina | |
| Aviv 215 S circular dichroism spectrometer | Aviv | |
| BLItz system | ForteBio | |