KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-Dscam IC | Schmucker Lab | N/A |
| Mouse anti-Fasciclin II | Developmental Studies Hybridoma Bank (DSHB) | DSHB Cat# 1D4; RRID: AB_528235 |
| Rat monoclonal anti-Elav | DSHB | DSHB Cat# 7E8A10; RRID: AB_528218 |
| Mouse monoclonal anti-Elav | DSHB | DSHB Cat# 9F8A9; RRID: AB_528217 |
| Mouse monoclonal anti-alpha-tubulin | DSHB | DSHB Cat# 12G10; RRID: AB_1157911 |
| Mouse monoclonal anti-Actin | DSHB | DSHB Cat# JLA20; RRID: AB_528068 |
| Cy3 Sheep Anti-Mouse IgG (H+L) | Jackson ImmunoResearch | Cat# 515-165-003; RRID: AB_2340315 |
| Peroxidase AffiniPure Goat Anti-Rabbit IgG (H+L) | Jackson ImmunoResearch | Cat# 111-035-003; RRID: AB_2313567 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Proteinase K | Invitrogen | Cat# 25530015 |
| RNaseOUT Recombinant Ribonuclease Inhibitor | Invitrogen | Cat# 10777–019 |
| Pierce Protease Inhibitor | Invitrogen | Cat# 88666 |
| Effectene transfection reagent | QIAGEN | Cat# 301425 |
| Maxima Reverse Transcriptase | ThermoFisher | Cat# EP0741 |
| SYBR Green PCR Master Mix | Invitrogen | Cat# 4309155 |
| Amersham Megaprime DNA Labeling System | GE Healthcare | Cat# RPN1606 |
| HiFi Assembly Cloning Kit | NEB | Cat# E2621 |
| lysozyme | Sigma | Cat# L6876 |
| Critical Commercial Assays | ||
| Dynabeads Protein G Immunoprecipitation Kit | Invitrogen | Cat#1007D |
| SQK-LSK108 Ligation Sequencing Kit 1D | Oxford Nanopore Technologies | Cat# SQK-LSK108 |
| EXP-PBC001 PCR Barcoding Kit I | Oxford Nanopore Technologies | Cat# EXP-PBC001 |
| Deposited Data | ||
| Nanopore Long-read sequencing raw data for Dscam1-L from exon 16 through extened 3′UTR | This paper | SAMN11457160, SAMN11457161, SAMN11457162 |
| 6–8 hr after egg laying embryos RNA-seq | Berkeley Drosophila Genome Project (BDGP) | SRX246422 |
| 16–18 hr embryos RNA-seq | BDGP | SRX246418 |
| L3 CNS RNA-seq | BDGP | SRR070410 |
| 4–6 hr embryos RNA-seq | BDGP | SRX246408 |
| 8–10 hr embryos RNA-seq | BDGP | SRX246409 |
| 14–16 hr embryos RNA-seq | BDGP | SRX246412 |
| Experimental Models: Cell Lines | ||
| D. melanogaster: Cell line S2: S2-DRSC | Drosophila Genomics Resource Center (DGRC) | Cat# 6 |
| Experimental Models: Organisms/Strains | ||
| UAS-sh-Dscam1-ext | This paper | N/A |
| Dscam1 ΔL | This paper | N/A |
| UAS-sh+19 | Bing Ye Lab | N/A |
| UAS-sh-19 | Bing Ye Lab | N/A |
| Elav-GAL4; UAS-Dicer2 | Eric Lai Lab | N/A |
| UAS-shElav | Bloomington Drosophila Stock Center (BDSC) | BL28371 |
| UAS-shFne | Vienna Drosophila Resource Center (VDRC) | VDRC-101508 |
| Pdf-GAL4; UAS-mCD8::EGFP | Yong Zhang Lab | N/A |
| repo-GAL4 | BDSC | BL#7415 |
| Elav-lexA | BDSC | BL#52676 |
| 20XUAS-6XmCherry | BDSC | BL#52267 |
| 13XlexAOP-GFP | BDSC | BL#32203 |
| Oligonucleotides | ||
| Primers for northern, RT-qPCR, and PCR see Table S1 | This paper | Table S1 |
| Primers to generate shRNA for Dscam1-ext | This paper | N/A |
| Forward: 5′- GATCGCTAGCAGTAGGCGTTTAGTTT | ||
| CACTTCAATAGTTATATTCAAGCAT A-3′; | ||
| Reverse: 5′-GATCGAATTCGCAGGCGTTTAGTTT | ||
| CACTTCAATATGCTTGAATATAACT A-3′. | ||
| Recombinant DNA | ||
| pWALLIUM20 | Harvard Medical School | N/A |
| Ubi-GAL4 | Eric Lai Lab | N/A |
| pUASTattB | Eric Lai Lab | N/A |
| pUASTattB_EGFP_SV40 | Jung H Kim Lab | N/A |
| pUAST-HA-elav | This paper | N/A |
| pUASTattB_EGFP_Dscam1–3′ UTR | This paper | N/A |
| pUASTattB_mini-gene_S | This paper | N/A |
| pUASTattB_mini-gene_L_only | This paper | N/A |
| pDEST60-Elav | This paper | N/A |
| Software and Algorithms | ||
| ImageJ | Schindelin et al., 2012 | https://fiji.sc/ |
| Albacore 2.0.1 | Oxford Nanopore Technologies | https://community.nanoporetech.com/downloads |
| Isocount 1.1.0 | Matthew Bauer | https://github.com/bauersmatthew/isocount |
| Porechop version 0.2.3 | Ryan Wick | https://github.com/rrwick/Porechop |