KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| Rabbit polyclonal Halotag antibody | Promega | G9281 |
|
| ||
| Rabbit anti-mouse IgG H&L | Abcam | ab46540 |
|
| ||
| Ginea pig α-rabbit antibody | Antibodie s online | ABIN101961 |
|
| ||
| Chemicals peptides and recombinant proteins | ||
|
| ||
| DSG (disuccinimidyl glutarate) | Thermo Fisher Scientific | 20593 |
|
| ||
| EGS (ethylene glycol bis(succinimidyl succinate)) | Thermo Fisher Scientific | 21565 |
|
| ||
| E. coli Spike-in DNA | EpiCypher | 18–1401 |
|
| ||
| pAG-Tn5 | EpiCyphe r | 15–1117 |
|
| ||
| Ampure XP beads | Beckman Coulter | A63880 |
|
| ||
| Hoechst 33342 | Sigma-Aldrich | 23491–52-3 |
|
| ||
| UltraPure™ SSC, 20X | Thermo Fisher Scientific |
15557044 |
|
| ||
| ProLong Gold Antifade Mountant | Thermo Fisher Scientific |
P36934 |
|
| ||
| TRIzol Reagents | Thermo Fisher Scientific |
15596026 |
|
| ||
| Critical commercial assays | ||
|
| ||
| HCR buffer set | Molecular Instruments |
www.molecularinstruments.com |
|
| ||
| HCR B1 488 amplifier | Molecular Instruments |
www.molecularinstruments.com |
|
| ||
| HCR B2 546 amplifier | Molecular Instruments | www.molecularinstruments.com |
|
| ||
| Deposited data | ||
|
| ||
| Micro-C for GAF depletion in embryo and Halo-Trl mutants | This study | GSE218168 |
|
| ||
| CUT&Tag for Halo-Trl mutants | This study | GSE218168 |
|
| ||
| RNA-seq for Halo-Trl mutants | This study | GSE218168 |
|
| ||
| Ph, Pc, Pho ChIP-seq | Brown et al., 2018 | GSE102339 |
|
| ||
| GAF ChIP-seq | Oh et al., 2013 | GSE38594 |
|
| ||
| CP190 ChIP-seq | Kyrchano va et al.,2021 | GSE175402 |
|
| ||
| Images for HCR in situ and GAF depletion effeciency | This study | DOI: 10.17632/g4w8kxv2xh.2 |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| Drosophila melanogaster/ Halo-Trl | Tang et al., 2022 | N/A |
|
| ||
| Drosophila melanogaster/ Halo-Trl ΔPOZ 90−119 /TM6B | Tang et al., 2022 | N/A |
|
| ||
| Drosophila melanogaster/ Halo-Trl ΔQ | Tang et al., 2022 | N/A |
|
| ||
| Drosophila melanogaster/ sfGFP-Trl(N) | Gaskill et al., 2021a | N/A |
|
| ||
| Drosophila melanogaster/ nos-deGradFP; sfGFP-Trl(N)/TM6C | Gaskill et al., 2021a | N/A |
|
| ||
| Oligonucleotides | ||
|
| ||
| tsh probe | Molecular Instruments | www.molecularinstruments.com |
|
| ||
| tio probe | Molecular Instruments | www.molecularinstruments.com |
|
| ||
| Software and algorithms | ||
|
| ||
| BWA | Li and Durbin, 2009 | https://bio-bwa.sourceforge.net/ |
|
| ||
| pairtools | Goloboro dko et al., 2019 | https://github.com/open2c/pairtools |
|
| ||
| Cooler | Abdennur and Mirny, 2020 | https://github.com/open2c/cooler |
|
| ||
| HiGlass | Kerpedjiev et al., 2018 | https://higlass.io/ |
|
| ||
| SIP | Rowley et al., 2020 | https://github.com/PouletAxel/SIP |
|
| ||
| BEDtools | Quinlan and Hall,2010 | https://bedtools.readthedocs.io/en/latest/ |
|
| ||
| DESeq2 | Love et al., 2017 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
|
| ||
| ggplot2 | Villanueva and Chen, 2019 | https://ggplot2.tidyverse.org/ |
|
| ||
| cooltools | Sergey, 2022 | https://github.com/open2c/cooltools |
|
| ||
| deepTools | Ramírez et al.,2014 | https://deeptools.readthedocs.io/en/develop/ |
|
| ||
| nf-core/cutandrun v2.0 | Cheshire and West | https://nf-co.re/cutandrun |
|
| ||
| SEACR | Meers et al., 2019 | https://github.com/FredHutch/SEACR |
|
| ||
| HOMER | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
|
| ||
| featureCounts | Liao et al., 2014 | https://subread.sourceforge.net/ |
|
| ||
| Bowtie2 | Langmead and Salzberg, 2012 | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
|
| ||
| SAMtools | Li et al., 2009 | http://www.htslib.org/ |
|
| ||
| MACS3 | Liu, 2015 | https://github.com/macs3-project/MACS |
|
| ||
| UCSC-tools | Kuhn et al., 2013 | https://genome.ucsc.edu/util.html |
|
| ||
| RNASTAR | Widmann et al., 2012 | https://github.com/alexdobin/STAR |
|
| ||
| ImageJ | Collins, 2007 | https://imagej.nih.gov/ij/ |
|
| ||
| t-test | Microsoft Office Excel | N/A |
|
| ||
| Linear regression | R | https://www.r-project.org/ |