KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-Nup98 | Capelson et al., 2010 | N/A |
| Rabbit polyclonal anti-Elys | This study | N/A |
| Guinea pig polyclonal anti-Nup93 | This study | N/A |
| Mouse monoclonal anti-EcR | Developmental Studies Hybridoma Bank | clone DDA2.7 |
| Mouse monoclonal anti-Tubulin | Developmental Studies Hybridoma Bank | clone E7 |
| Mouse monoclonal anti-Mtor | gift from Prof. K.M. Johansen (Iowa State University) | clone 12F10 |
| Mouse monoclonal anti-Lamin | Developmental Studies Hybridoma Bank | clone ADL101 |
| Rabbit polyclonal anti-Lamin | gift from Prof. P.A. Fisher (Stony Brook University) | N/A |
| Rabbit polyclonal anti-Nxf1 | gift from Prof. E. Izaurralde (MPI for Developmental Biology) | N/A |
| Rabbit polyclonal anti-Trr | gift from Prof. A. Mazo (Thomas Jefferson University) | N/A |
| Rabbit polyclonal anti-histone H3 | gift from Prof. S.L. Berger (University of Pennsylvania) | Abcam ab1791; RRID: AB_302613 |
| Rabbit polyclonal anti-CTCF | gift from Prof. V.G. Corces (Emory University) | N/A |
| Rabbit polyclonal anti-CP190 | gift from Prof. V.G. Corces (Emory University) | N/A |
| Rabbit polyclonal anti-SuHw | gift from Prof. V.G. Corces (Emory University) | N/A |
| Rabbit polyclonal anti-GAF | gift from Prof. V.G. Corces (Emory University) | N/A |
| Rabbit polyclonal anti-histone H3K27Acetyl | Active Motif | #39133; RRID: AB_2561016 |
| Rabbit polyclonal anti-histone H3K27Me3 | Active Motif | #39155; RRID: AB_2561020 |
| Mouse monoclonal anti-Nuclear Pore Complex proteins | Covance | clone MAb414 |
| Sheep polyclonal anti-Digoxigenin-AP | Roche | #11 207 741 910 |
| Bacterial and Virus Strains | ||
| E. Coli: BL21 competent | NEB | C2530H |
| Biological Samples | ||
| Drosophila third-instar larvae brains | This study | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 20-Hydroxyecdysone | Sigma-Aldrich | H5142 |
| TransIT-Insect Reagent | Mirus Bio LLC | MIR6100 |
| Fugene HD | Promega | E2311 |
| MEGAscript T7 Transcription kit | Thermo Fisher Scientific | AM1334 |
| OneStep RT-PCR kit | QIAGEN | cat#210212 |
| Power SYBR Green PCR Master mix | Applied Biosystems | cat#4367659 |
| DIG-Nick Translation mix | Roche | #11 745 816 910 |
| Protein A Agarose | Thermo Fisher Scientific | cat#15918014 |
| Protein G Agarose | Thermo Fisher Scientific | cat#15920010 |
| Dynabeads M-280 Sheep anti-Rabbit | Thermo Fisher Scientific | cat#11204D |
| Dynabeads M-280 Sheep anti-Mouse | Thermo Fisher Scientific | cat#11203D |
| Critical Commercial Assays | ||
| NEBNext Ultra DNA Library Prep Kit for Illumina 96 rxn | NEB | E7370L |
| NEBNext Multiplex Oligos for Illumina | NEB | Set1: E7335L |
| (Index Primers Set 1 and Set 2) 96 rxn | Set2: E7500L | |
| NextSeq 500/550 High Output v2 kit (75 cycles) | Illumina | FC-404-2005 |
| Deposited Data | ||
| ChIP-seq raw and analyzed data | This study | GSE94922 |
| Experimental Models: Cell Lines | ||
| S2-DRSC | Drosophila Genomics Resource Center | Flybase: FBrf0024118 |
| Experimental Models: Organisms/Strains | ||
| Nup98-96 allele: | Bloomington Drosophila | BDSC: 28433 |
| y[1] w[*]; P{w[+mC] = EP}Nup98-96 [G2120]/TM3, Sb[1] Ser[1] | Stock Center | |
| Nup98-96 allele: | Bloomington Drosophila | BDSC: 4951 |
| Nup98-96[339]/TM3, Sb[1] | Stock Center | |
| Gypsy insertion CtK: y[1] ct[K]; bw[1] | Bloomington Drosophila Stock Center | BDSC: 171 |
| Oregon-R | Bloomington Drosophila Stock Center | BDSC: 5 |
| Oligonucleotides | ||
| 3C primers | IDT | see Table S6 |
| Digestion efficiency primers | IDT | see Table S6 |
| Expression analysis primers | IDT | see Table S6 |
| dsRNA primers | IDT | see Table S6 |
| oligo-(dT)40-Cy3 | IDT | |
| Recombinant DNA | ||
| pNup98-Myc | Pascual-Garcia et al., 2014 | N/A |
| p-Myc (pAWM) | Carnegie Institution for Science | https://emb.carnegiescience.edu/Drosophila-gateway-vector-collection |
| pDEST15 | Thermo Fisher Scientific | cat#11802014 |
| pETG-41-A | EMBL | https://www.embl.de/pepcore/pepcore_services/strains_vectors/vectors/gateway_vectors/ |
| cDNA LD21129 | Drosophila Genomics Resource Center | Flybase: FBcl0172220 |
| BAC DNA clone BACN14N24 | BACPAC Resource Center | EDROSBAC-14N24 |
| BAC DNA clone BACN04G20 | BACPAC Resource Center | EDROSBAC-4G20 |
| BAC DNA clone BACR04K01 | BACPAC Resource Center | RP98-4K1 |
| BAC DNA clone BACR28H1 | BACPAC Resource Center | RP98-28H1 |
| BAC DNA clone BAC RP98-15I7 | BACPAC Resource Center | RP98-15I7 |
| Software and Algorithms | ||
| 3C primer design (3PD) | Fröhler and Dieterich, 2009 | http://3pd.mdc-berlin.de/ |
| Fiji | https://fiji.sc/ | |
| Leica Application Suite X | Leica software | http://www.leica-microsystems.com/products/microscope-software/software-for-life-science-research/las-x-powerful-and-flexible/ |
| NIS-Elements | Nikon software | http://www.nikonmetrology.com/en_US/Products/Software/Imaging-Software/NIS-Elements-Microscope-Imaging-Software |
| Prism | GraphPad software | https://www.graphpad.com/scientific-software/prism/ |
| NCBI SRA Toolkit | https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/ | |
| Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| MACS2 | Feng et al., 2012 | https://github.com/taoliu/MACS |
| R | The R Project for Statistical Computing | https://www.r-project.org/ |
| R package DiffBind | Stark and Brown, 2011 | https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| HOMER | Heinz et al., 2010 | http://homer.salk.edu/homer/ |
| IGV | Thorvaldsdóttir et al., 2013 | http://software.broadinstitute.org/software/igv/ |
| BEDtools | Quinlan and Hall, 2010 | http://bedtools.readthedocs.io/en/latest/ |