Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | anti-SXL (Mouse monoclonal) | Developmental Studies Hybridoma Bank | Cat# M18-s, RRID:AB_528464 | IF(1:100) |
| Antibody | anti-MSL2 (Goat monoclonal) | Santa Cruz | Cat# sc-32459, RRID:AB_672213 | IF(1:100) |
| Antibody | anti-MOF (Goat monoclonal) | Santa Cruz | Cat# sc-22351, RRID:AB_670132 | IF(1:100) |
| Antibody | anti-H3 (Rabbit polyclonal) | Novus | Cat# NB500-171, RRID:AB_10001790 | WB(1:1000) |
| Antibody | anti-H4K16Ac (Rabbit monoclonal) | EMD Millipore | Cat# 07-329, RRID:AB_310525 | IF(1:100) WB(1:1000) |
| Antibody | anti-Digoxigenin (Mouse monoclonal) | Jackson Immuno Research | Cat# 200-062-156, RRID:AB_233901 | TSA-FISH(1:400) |
| Antibody | Streptavidin-HRP (Rabbit polyclonal) | Invitrogen | Cat# S991 | TSA-FISH(1:1000) |
| Sequence-based reagent | Ime4-L | This paper | PCR primers | CAAGTACGTGCACTATGAGG |
| Sequence-based reagent | Ime4-R | This paper | PCR primers | GTCATGTCCAAGAAGCGTAG |
| Sequence-based reagent | dMettl14-L | This paper | PCR primers | GCCTCTTCCTCCAAGAAAAC |
| Sequence-based reagent | dMettl14-R | This paper | PCR primers | CCTCAACTTGGGATACTCCT |
| Sequence-based reagent | fl(2)d-L | This paper | PCR primers | CCTGGACGTTATTTCCTACT |
| Sequence-based reagent | fl(2)d-R | This paper | PCR primers | TAAGCTAGAGACCATTCACG |
| Sequence-based reagent | vir-L | This paper | PCR primers | GTACATGAAACCCTTAGAGGC |
| Sequence-based reagent | vir-R | This paper | PCR primers | CTTGCTTATGGAGAGATAGCG |
| Sequence-based reagent | nito-L | This paper | PCR primers | GCCAGTACGGTTCCAGATGT |
| Sequence-based reagent | nito-R | This paper | PCR primers | CCGTCCGTCAAATGAAACTT |
| Sequence-based reagent | Ythdc1-L | This paper | PCR primers | GGTCGTGATTTGATCCTCTG |
| Sequence-based reagent | Ythdc1-R | This paper | PCR primers | TCGAACTCACTCCCATACTC |
| Sequence-based reagent | tubulin-F | This paper | PCR primers | AGCTCAGCACCCTCTGTGTAAT |
| Sequence-based reagent | tubulin-R | This paper | PCR primers | AGCTGGAGCGCATCAATGTGTA |
| Sequence-based reagent | Ime4-F-T3 | This paper | FISH primers | TGTTGGGAAATCACTCCCAATTAAGAGAAGTTTAAGTCCCACGG |
| Sequence-based reagent | Ime4-R-T7 | This paper | FISH primers | GTAATACGACTCACTATAGGGAGACCACCATCTGGATAACGCTTCTGG |
| Sequence-based reagent | dMettl14-F-T3 | This paper | FISH primers | TGTTGGGAAATCACTCCCAATTAACCAATCCGCACAATGACTAC |
| Sequence-based reagent | dMettl14-R-T7 | This paper | FISH primers | GTAATACGACTCACTATAGGGAGACCACTAGCCAACCTGGTCGAATAC |
| Sequence-based reagent | fl(2)d-F-T3 | This paper | FISH primers | TGTTGGGAAATCACTCCCAATTAACTAGAGACCATTCACGAGGA |
| Sequence-based reagent | fl(2)d-R-T7 | This paper | FISH primers | GTAATACGACTCACTATAGGGAGACCACATTATGTATGTCTACGCCGC |
| Sequence-based reagent | vir-F-T3 | This paper | FISH primers | TGTTGGGAAATCACTCCCAATTAACGAAATGTCGTACAAGGTGC |
| Sequence-based reagent | vir-R-T7 | This paper | FISH primers | GTAATACGACTCACTATAGGGAGACCACGATCTCCGGGAAAAGTGGTT |
| Sequence-based reagent | nito-F-T3 | This paper | FISH primers | TGTTGGGAAATCACTCCCAATTAACTCCGATTGATCCCTACGAT |
| Sequence-based reagent | nito-R-T7 | This paper | FISH primers | GTAATACGACTCACTATAGGGAGACCACGTATCTCCGTCCGTCAAATG |
| Sequence-based reagent | Ythdc1-F-T3 | This paper | FISH primers | TGTTGGGAAATCACTCCCAATTAACGAATCGAATGGTGGAGACT |
| Sequence-based reagent | Ythdc1-R-T7 | This paper | FISH primers | GTAATACGACTCACTATAGGGAGACCACCCGTGTGTCTCGGAATAGGT |
| Commercial assay or kit | m6A RNA Methylation Quantification Kit (Colorimetric) | EpiQuik | P-9005–96 | |
| Commercial assay or kit | 2×EasyTaq PCR Super Mix (+Dye) | TransGen Biotech | AS111-12 | |
| Commercial assay or kit | TransTaq-T DNA Polymerase | TransGen Biotech | AP122 | |
| Commercial assay or kit | TransScript one-step gDNA Removal and cDNA Synthesis SuperMix | TransGen Biotech | AT311-03 | |
| Commercial assay or kit | TransStart Tip Green qPCR SuperMix (+Dye II) | TransGen Biotech | AQ142-24 | |
| Chemical compound, drug | Cyanine 3 Tyramide | Akoya Biosciences | FP1046 | |
| Chemical compound, drug | Proteinase K | Sigma | H4784 | |
| Chemical compound, drug | Heparin sodium salt | Sigma | P2308 | |
| Chemical compound, drug | Salmon sperm single-stranded DNA | Sigma | D9156 | |
| Chemical compound, drug | Digoxigenin-11-UTP | Sigma (Roche Diagnostics) | 11209256910 | |
| Chemical compound, drug | Ribonucleoside Triphosphate Set (NTP) | Sigma (Roche Diagnostics) | 11277057001 | |
| Chemical compound, drug | Donkey Serum | Solarbio | N/A | |
| Chemical compound, drug | 5×Transcription buffer | Thermo Scientific | N/A | |
| Chemical compound, drug | T7 RNA polymerase | Thermo Scientific | EP0111 | |
| Software, algorithm | R v4.2.2 | http://www.R-project.org | ||
| Software, algorithm | trim-galore v0.6.10 | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ | ||
| Software, algorithm | FastQC v0.12.1 | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | ||
| Software, algorithm | HISAT2 v2.2.1 | Kim et al., 2019 | ||
| Software, algorithm | StringTie v2.1.5 | Pertea et al., 2015 | ||
| Software, algorithm | exomePeak2 v1.10.0 | Meng et al., 2013 | ||
| Software, algorithm | HOMER v4.11 | Heinz et al., 2010 | ||
| Software, algorithm | DiffBind v3.8.4 | Stark and Brown, 2013 | ||
| Software, algorithm | ChIPseeker v1.34.1 | Yu et al., 2015 | ||
| Software, algorithm | deepTools v3.5.4 | Ramírez et al., 2014 | ||
| Software, algorithm | rMATS v4.2.0 | Shen et al., 2014 | ||
| Software, algorithm | ggplot2 v3.4.0 | Villanueva and Chen, 2019 | ||
| Software, algorithm | clusterProfiler v4.6.0 | Wu et al., 2021 | ||
| Software, algorithm | org.Dm.eg.db v3.16.0 | https://www.bioconductor.org/ | ||
| Software, algorithm | DESeq2 v1.38.2 | Love et al., 2014 | ||
| Software, algorithm | Integrative Genomics Viewer v2.12.0 | Thorvaldsdóttir et al., 2013 | ||
| Software, algorithm | Fiji v1.53c | Schindelin et al., 2012 | ||
| Software, algorithm | AnimalTFDB | Hu et al., 2019 | ||
| Other | DAPI stain | Sigma | 28718-90-3 | (1 µg/mL) |