1. Developmental Biology
  2. Genetics and Genomics

A genome-wide MAGIC kit for recombinase-independent mosaic analysis in Drosophila

  1. Yifan Shen
  2. Ann T Yeung
  3. Payton Ditchfield
  4. Elizabeth Korn
  5. Rhiannon Clements
  6. Xinchen Chen
  7. Bei Wang
  8. Zixian Huang
  9. Michael Sheen
  10. Parker A Jarman
  11. Chun Han  Is a corresponding author
  1. Department of Molecular Biology and Genetics, Cornell University, United States
  2. Weill Institute for Cell and Molecular Biology, Cornell University, United States
https://doi.org/10.7554/eLife.108453.3
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Cite this article
  1. Yifan Shen
  2. Ann T Yeung
  3. Payton Ditchfield
  4. Elizabeth Korn
  5. Rhiannon Clements
  6. Xinchen Chen
  7. Bei Wang
  8. Zixian Huang
  9. Michael Sheen
  10. Parker A Jarman
  11. Chun Han
(2026)
A genome-wide MAGIC kit for recombinase-independent mosaic analysis in Drosophila
eLife 14:RP108453.
https://doi.org/10.7554/eLife.108453.3
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5 figures, 2 tables and 2 additional files

Figures

Figure 1 with 1 supplement
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New gRNA-marker designs improve pMAGIC and nMAGIC.

(A) Original and new designs of gRNA-markers for pMAGIC and nMAGIC. (B) Comparison of clone frequency in larval sensory neurons between two gRNA designs. Clones were induced by zk-Cas9 (expressed in the embryonic ectoderm) and labeled by the pan-neuronal driver RabX4-Gal4>MApHS (MApHS: pHluorin-CD4-tdTomato). The number represents clones between A1 and A7 segments on one side of each larva. n=larvae number: tgFE (n=10), Qtg2.1 (n=10). (C–E) Labeling of hemocytes in whole 3rd instar larvae by pxn-Gal4>CD4-tdTom alone (C) or together with gRNA-42A4(Gal80)-uDEH (ubi-Gal80) (D) or gRNA-42A4(Gal80)-tDES (tub-Gal80) (E). The panels on the right show enlarged views of the boxed regions. (F) Designs of Gal80 variants tested in pMAGIC gRNA-markers. (G) The brightness of epidermal clones induced by zk-Cas9 and labeled by the epidermal driver R38F11-Gal4>tdTom in the presence of pMAGIC gRNA-markers. n=image numbers: gRNA-40D2-uH (n=32), gRNA-40D2-uDEH (n=31), gRNA-42A4-uDEH (n=52), gRNA-42A4-tDEH (n=39), gRNA-42A4-tDES (n=38). (H) The brightness of neuronal clones induced by zk-Cas9 and labeled by RabX4-Gal4>MApHS in the presence of pMAGIC gRNA-markers. The brightness of tdTom was measured and compared. n=neuron numbers: gRNA-40D2-uH (n=16), gRNA-40D2-uDEH (n=16), gRNA-42A4-uDEH (n=16), gRNA-42A4-tDEH (n=15), gRNA-42A4-tDES (n=16). (I) A portion of a larval wing disc containing nMAGIC clones visualized by nlsBFP. (J and J’) A portion of a wing disc containing nMAGIC clones labeled by cytosolic BFP (J) and HA staining (J’). (K) Epidermal clones on the larva body wall labeled by nlsBFP. (L) Epidermal clones visualized by cytosolic BFP. (M) A portion of a wing disc containing nMAGIC clones labeled by cytosolic miRFP680 (IFP). (O) Sizes of nMAGIC BFP/BFP clones and wild-type (+/+) clones in wing discs. Two types of clones in the same discs were connected. n=wing disc number: BFP/BFP (n=18), +/+ (n=18). In all plots, black bar, mean; red bar, SD; AU, arbitrary unit. Student’s t-test in (B); one-way analysis of variance (ANOVA) and Tukey’s honest significant difference (HSD) test in (G) and (H). paired t-test in (O) *p≤0.05, **p≤0.01, ***p≤0.001, ns, not significant. For (C–E), scale bar, 300 µm. For (I–M), scale bar, 100 µm.

Figure 1—figure supplement 1
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MAGIC principles.

(A) A diagram of MAGIC principle. This diagram is based on a hypothetic cell that contains a GFP (green) marker and an RFP (red) marker on two homologous chromosomes. Co-existence of the two markers renders the cell yellow, while their segregation through mitotic recombination results in red-only and green-only twin-spot daughter cells. (B) Diagrams of positive MAGIC (pMAGIC) and negative MAGIC (nMAGIC). pMAGIC involves ubiquitously expressed Gal80 that suppresses Gal4-driven expression of a fluorescent marker in Gal80-containing cells. Only homozygous cells lacking the gRNA marker will be labeled. nMAGIC utilizes ubiquitously expressed BFP to distinguish two populations of twin-spot cells, one with two copies of BFP and the other lacking BFP entirely. (C) An example crossing scheme of pMAGIC experiments. This example uses the epidermal R38F11-Gal4 to drive expression of tdTom and the epidermal/neuronal progenitor zk-Cas9 to induce clones. For the convenience of the experiment, R38F11-Gal4, UAS-tdTom, and zk-Cas9 have been recombined onto the same chromosome.

Figure 2
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A genome-wide gRNA-marker kit suits diverse needs of clone frequency.

(A) Scheme of gRNA-marker insertion sites and target sites on Drosophila chromosomes. (B) Comparison of clone frequencies of all pMAGIC gRNA-markers in larval sensory neurons, clones are labeled using RabX4-Gal4>MApHs (for Chromosome X, II, and IV) or 21–7 Gal4 UAS-MApHS (for Chromosome III). n=larvae number: X2 (n=10), 20F2 (n=10), 20F1 (n=10), 40D2 (n=20), 40D4 (n=10), 40E1 (n=10), 41F9 (n=20), 41F11 (n=10), 42A4 (n=10), 80C1 (n=20), 80C2 (n=14), 80F5 (n=15), 81 F (n=10), 82A4 (n=10), 82C3 (n=10), 101F1a (n=10), 101F1b (n=10), 101F1c (n=10). (C) Comparison of clone areas in larval wing discs labeled by nMAGIC gRNA markers on 2 R. n=wing disc number: 41F9 (n=14), 41F11 (n=16), 42A4 (n=15). (D and E) Neuronal clones in the central part of the adult brain induced by ey-Cas9 (expressed in progenitor cells of many neuronal tissues) and labeled by RabX4-Gal4>MApHS along with pMAGIC gRNA-markers gRNA-40D2 (D) and gRNA-40E1 (E). MApHS contains pHluorin and tdTom (Han et al., 2014), but only the tdTom channel is shown. In all plots, black bar, mean; red bar, SD. One-way ANOVA and Tukey’s HSD test. *p≤0.05, **p≤0.01, ***p≤0.001, ns, not significant. For (D) and (E), scale bar 100 µm.

Figure 3
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MAGIC allows clonal analysis in diverse tissues and cell types.

(A–F) pMAGIC clones induced in different tissues by vas-Cas9 (ubiquitous Cas9) gRNA-40D2(Gal80) and labeled by tub-Gal4 UAS-CD8-GFP (green). DAPI staining (white) shows all nuclei. (G) A pMAGIC epidermal clone on the larval body wall induced by zk-Cas9 gRNA-40D2(Gal80) and labeled by R38F11-Gal4>tdTom (green). Epidermal junctions are labeled by α-Catenin-GFP (white). (H) pMAGIC glia clones in the larval brain induced by gcm-Cas9 (expressed in glial precursor genes) gRNA-40D2(Gal80) and labeled by repo-Gal4 UAS-CD8-GFP (green). Glial nuclei are labeled by Repo staining (white). (I) pMAGIC hemocyte clones induced by Act-Cas9 gRNA-40D2(Gal80) and labeled by pxn-Gal4>CD4-tdTom. (J-K’) pMAGIC clones in adult brain induced by hs-Cas9 gRNA-40D2(Gal80) and labeled by RabX4-Gal4>MApHS. Heat shock was performed at 120 hr after egg lay (AEL) (J-J’) and 48 hr after puparium formation (APF) (K-K’). The boxed areas were enlarged to show clones in the mushroom body and lateral horn region. Only the tdTom channel is shown. In (A), (D–F), (H), (J), and (K), scale bar 100 µm; in (B–C), (G), (J’), and (K’), scale bar 50 µm; in (I), scale bar 25 µm.

Figure 4
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MAGIC facilitates clonal analysis at the NMJ.

(A-A”) pMAGIC clones of VGlut1 mutation in motor neurons at the neuromuscular junction. Clones were induced by zk-Cas9 gRNA-40D2(Gal80) and labeled by tub-Gal4>CD8 GFP. The loss of VGlut is confirmed by VGlut staining. The mutant clones are outlined in (A”). (B-B”) A pMAGIC clone of brpd09839 mutation in a motor neuron at the neuromuscular junction. Clones were induced by zk-Cas9 gRNA-42A4(Gal80) and labeled by tub-Gal4>CD8 GFP. The loss of Brp is confirmed by Brp staining. The mutant clone is outlined in (B”). In both experiments, HRP staining shows all axons. Scale bars, 10 µm.

Figure 5 with 1 supplement
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MAGIC enables clonal analysis of pericentromeric genes, 4th chromosome-associated mutations, and in interspecific hybrid animals.

(A) A WT pMAGIC class IV da neuron clone exhibiting complete dendrite pruning at 16 hr APF. (B–D) pMAGIC clones of EcRM554fs mutation in da neurons imaged at 16 hr APF, exhibiting the lack of pruning (B and D) or apoptosis (C). In (A–D), the clones were induced by zk-cas9 with gRNA-41F9(Gal80) and labeled by RabX4-Gal4>MApHS. Neuronal cell bodies are indicated by arrows. Only the tdTom channel is shown. The signals in epidermal cells (A) were due to engulfment of pruned dendrites by epidermal cells (Han et al., 2014). (E and F) WT (E) and Df(4)ED6380 (F) pMAGIC clones in C4da neurons induced by zk-cas9 gRNA-101Fc(Gal80) and labeled by RabX4-Gal4>MApHS. Only the tdTom channel is shown. (G) Normalized dendrite length of WT clones and deficiency clones. Black bar, mean; red bar, SD. Student’s t-test. ***≤0.001. (H) Scheme for interspecific crosses between D. melanogaster (D.m) and D. simulans (D.s). (I and J) Wing discs from male (I) and female (J) progeny carrying clones. Scale bars, 50 µm.

Figure 5—figure supplement 1
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Transgenic markers on the 4th chromosome show uneven expression.

(A–B) Representative epidermal (A) and wing disc (B) images showing uneven expression of gRNA-101F1c(BFP) inserted at attP102D on the 4th chromosome. Yellow arrowheads point to cells lacking BFP expression. Scale bars, 50 µm. (C) Frequency of labeled neurons by indicated gRNA (Gal80) in the absence and presence of Cas9. The zk-Cas9 dataset is the same as that for chromosome 4 in Figure 2B. Black bar, mean; red bar, SD. One-way ANOVA and HSD test. ***p≤0.001.

Tables

Table 1
gRNA-marker collection.
Chr ArmTarget sitegRNA locationpMAGIC vectornMAGIC vectorClone frequencyBDSC IDs ‡
2L40D2attP[VK00037]pAC-U63-gRNA2.1-ubiGal80(DE)-His2AvpAC-U63-tgRNA-nlsBFP* pAC-U63-gRNA2.1-tub-miRFP680-T2A-HO1(HA) (HA)31606005 and 92741
2L40D4attP[VK00037]pAC-U63-tgRNA-Gal80*pAC-U63-tgRNA-nlsBFP*1392744 and 92742
2L40E1attP[VK00037]pAC-U63-tgRNA-Gal80*pAC-U63-tgRNA-nlsBFP*4606004 and 606003
2R41F9attP[VK00018]pAC-U63-gRNA2.1-ubiGal80(DE)-His2AvpAC-U63-gRNA2.1-tubBFP(HA)10606006 and 606010
2R41F11attP[VK00018]pAC-U63-gRNA2.1-ubiGal80(DE)-His2AvpAC-U63-gRNA2.1-tubBFP(HA)14606007 and 606009
2R42A4attP[VK00018]pAC-U63-gRNA2.1-tubGal80(DE)-SV40pAC-U63-gRNA2.1-tubBFP(HA)14606008 and 606011
3L80F5attP2pAC-U63-gRNA2.1-tubGal80(DE)-His2AvpAC-U63-gRNA2.1-tubBFP(HA)11606014 and 606017
3L80C2attP2pAC-U63-gRNA2.1-tubGal80(DE)-His2AvpAC-U63-gRNA2.1-tubBFP(HA)7606013 and 606016
3L80C1attP2pAC-U63-gRNA2.1-tubGal80(DE)-His2AvpAC-U63-gRNA2.1-tubBFP(HA)4606012 and 606015
3R81 FattP[VK00027]pAC-U63-gRNA2.1-tubGal80(DE)-His2AvpAC-U63-gRNA2.1-tubBFP(HA)4606020 and 606021
3R82A4attP[VK00027]pAC-U63-gRNA2.1-tubGal80(DE)-His2AvpAC-U63-gRNA2.1-tubBFP(HA)10606018 and 606022
3R82C3attP[VK00027]pAC-U63-gRNA2.1-tubGal80(DE)-His2AvpAC-U63-gRNA2.1-tubBFP(HA)16606019 and 606023
XX2attP18pAC-U63-gRNA2.1-tubGal80(DE)-SV40pAC-U63-gRNA2.1-tubBFP(HA)19606024 and 606028
X20F1attP18pAC-U63-gRNA2.1-tubGal80(DE)-SV40pAC-U63-gRNA2.1-tubBFP(HA)18606025 and 606779
X20F2attP18pAC-U63-gRNA2.1-tubGal80(DE)-SV40pAC-U63-gRNA2.1-tubBFP(HA)19606026 and 606029
IV101F1-aattP[ZH-102D]†pAC-U63-gRNA2.1-tubGal80(DE)-SV40pAC-U63-gRNA2.1-tubBFP(HA)4606776 and 606780
IV101F1-battP[ZH-102D]†pAC-U63-gRNA2.1-tubGal80(DE)-SV40pAC-U63-gRNA2.1-tubBFP(HA)25606777 and 606781
IV101F1-cattP[ZH-102D]†pAC-U63-gRNA2.1-tubGal80(DE)-SV40pAC-U63-gRNA2.1-tubBFP(HA)28606778 and 606782

  1. Clone frequencies are measured by averaging clone numbers in 10 laterally mounted 3rd instar larvae with pMAGIC gRNA-markers. Only clones in A1 to A7 segments of one side of each larva were counted.

  2. *

    Previously published gRNA-markers.

  3. †

    3xP3-RFP has been removed from these lines.

  4. ‡

    Detailed information for each line is available at https://bdsc.indiana.edu/stocks/misc/magic.html.

Appendix 1—key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Genetic reagent (D. melanogaster)gRNA-40D2-tgFE-uHAllen et al., 2021w; gRNA-40D2-tgFE-uHVK00037
Genetic reagent (D. melanogaster)gRNA-40D2-Qtg2.1-uDEHThis studyRRID:BDSC_606005w; gRNA-40D2-Qtg2.1-uDEHVK00037; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-40D4-tgFE-uHAllen et al., 2021w; gRNA-40D4-tgFE-uHVK00037
Genetic reagent (D. melanogaster)gRNA-40E1-tgFE-uHAllen et al., 2021RRID:BDSC_606004w; gRNA-40E1-tgFE-uHVK00037
Genetic reagent (D. melanogaster)gRNA-42A4-Qtg2.1-uDEHThis studyw; gRNA-42A4-Qtg2.1-uDEHVK00018; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-41F9-Qtg2.1-uDEHThis studyRRID:BDSC_606006w; gRNA-41F9-Qtg2.1-uDEHVK00018; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-41F11-Qtg2.1-uDEHThis studyRRID:BDSC_606007w; gRNA-41F11-Qtg2.1-uDEHVK00018; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-42A4-Qtg2.1-tDEHThis studyw; gRNA-42A4-Qtg2.1-tDEHVK00018; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-42A4-Qtg2.1-tDESThis studyRRID:BDSC_606008w; gRNA-42A4-Qtg2.1-tDESVK00018; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-80F5-Qtg2.1-tDEHThis studyRRID:BDSC_606014w; gRNA-80F5-Qtg2.1-tDEHattP2; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-80C2-Qtg2.1-tDEHThis studyRRID:BDSC_606013w; gRNA-80C2-Qtg2.1-tDEHattP2; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-80C1-Qtg2.1-tDEHThis studyRRID:BDSC_606012w; gRNA-80C1-Qtg2.1-tDEHattP2; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-81F-Qtg2.1-tDEHThis studyRRID:BDSC_606020w; gRNA-81F-Qtg2.1-tDEHVK00027; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-82A4-Qtg2.1-tDEHThis studyRRID:BDSC_606018w; gRNA-82A4-Qtg2.1-tDEHVK00027; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-82C3-Qtg2.1-tDEHThis studyRRID:BDSC_606019w; gRNA-82C3-Qtg2.1-tDEHVK00027; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-X2-Qtg2.1-tDESThis studyRRID:BDSC_606024w; gRNA-X2-Qtg2.1-tDESattP18; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-20F1-Qtg2.1-tDESThis studyRRID:BDSC_606025w; gRNA-20F1-Qtg2.1-tDESattP18; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-20F2-Qtg2.1-tDESThis studyRRID:BDSC_606026w; gRNA-20F2-Qtg2.1-tDESattP18; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-101F1a-Qtg2.1-tDESThis studyRRID:BDSC_606776w; gRNA-101F1a-Qtg2.1-tDESattP[102D]; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-101F1b-Qtg2.1-tDESThis studyRRID:BDSC_606777w; gRNA-101F1b-Qtg2.1-tDESattP[102D]; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-101F1c-Qtg2.1-tDESThis studyRRID:BDSC_606778w; gRNA-101F1c-Qtg2.1-tDESattP[102D]; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-40D2-nlsBFPAllen et al., 2021w; gRNA-40D2-nlsBFPVK00037
Genetic reagent (D. melanogaster)gRNA-40D4-nlsBFPAllen et al., 2021w; gRNA-40D4-nlsBFPVK00037
Genetic reagent (D. melanogaster)gRNA-40E1-nlsBFPAllen et al., 2021RRID:BDSC_606003w; gRNA-40E1-nlsBFPVK00037
Genetic reagent (D. melanogaster)gRNA-40D2-tub-IFP-HAThis studyw; gRNA-40D2-tub-IFP-HAVK00037; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-42A4-tub-BFP-HAThis studyRRID:BDSC_606011w; gRNA-42A4-tub-BFP-HAVK00018; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-41F9-tub-BFP-HAThis studyRRID:BDSC_606010w; gRNA-41F9-tub-BFP-HAVK00018; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-41F11-tub-BFP-HAThis studyRRID:BDSC_606009w; gRNA-41F11-tub-BFP-HAVK00018; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-80F5-tub-BFP-HAThis studyRRID:BDSC_606017w; gRNA-80F5-tub-BFP-HAattP2; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-80C2-tub-BFP-HAThis studyRRID:BDSC_606016w; gRNA-80C2-tub-BFP-HAattP2; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-80C1-tub-BFP-HAThis studyRRID:BDSC_606015w; gRNA-80C1-tub-BFP-HAattP2; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-81F-tub-BFP-HAThis studyRRID:BDSC_606021w; gRNA-81F-tub-BFP-HAVK00027; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-82A4-tub-BFP-HAThis studyRRID:BDSC_606022w; gRNA-82A4-tub-BFP-HAVK00027; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-82C3-tub-BFP-HAThis studyRRID:BDSC_606023w; gRNA-82C3-tub-BFP-HAVK00027; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-X2-tub-BFP-HAThis studyRRID:BDSC_606028w; gRNA-X2-tub-BFP-HAattP18; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-20F1-tub-BFP-HAThis studyRRID:BDSC_606779w; gRNA-20F1-tub-BFP-HAattP18; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-20F2-tub-BFP-HAThis studyRRID:BDSC_606029w; gRNA-20F2-tub-BFP-HAattP18; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-101F1a-tub-BFP-HAThis studyRRID:BDSC_606780w; gRNA-101F1a-tub-BFP-HAattP[102D]; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-101F1b-tub-BFP-HAThis studyRRID:BDSC_606781w; gRNA-101F1b-tub-BFP-HAattP[102D]; in Materials and methods
Genetic reagent (D. melanogaster)gRNA-101F1c-tub-BFP-HAThis studyRRID:BDSC_606782w; gRNA-101F1c-tub-BFP-HAattP[102D]; in Materials and methods
Genetic reagent (D. melanogaster)pxn-Gal4Han et al., 2014
Genetic reagent (D. melanogaster)UAS-CD4-tdTomHan et al., 2011RRID:BDSC_35841UAS-CD4-tdTom7M1
Genetic reagent (D. melanogaster)hh-Cas9Poe et al., 2019R28E04-Cas96A
Genetic reagent (D. melanogaster)zk-cas9Allen et al., 2021zk-Cas9VK00037
Genetic reagent (D. melanogaster)hs-cas9Garcia-Marques et al., 2020
Genetic reagent (D. melanogaster)Gal421-7Han et al., 2011
Genetic reagent (D. melanogaster)UAS-MApHSHan et al., 2014UAS-MApHSVK00019
Genetic reagent (D. melanogaster)RabX4-Gal4Bloomington Drosophila Stock CenterRRID:BDSC_51602
Genetic reagent (D. melanogaster)R38F11-Gal4Bloomington Drosophila Stock CenterRRID:BDSC_50014R38F11-Gal4attP2
Genetic reagent (D. melanogaster)ey-Cas9Ji et al., 2022ey-Cas9VK00005
Genetic reagent (D. melanogaster)vas-cas9López Del Amo et al., 2022
Genetic reagent (D. melanogaster)tubP(FRT.stop)Gal4 UAS-Flp UAS-mCD8::GFPKoreman et al., 2021
Genetic reagent (D. melanogaster)α-Catenin-GFPBloomington Drosophila Stock CenterRRID:BDSC_58787w[*]; P{w[+mC]=UAS-alpha-Cat.T:GFP.sg}3/CyO
Genetic reagent (D. melanogaster)gcm-Cas9Chen et al., 2024
Genetic reagent (D. melanogaster)repo-Gal4Bloomington Drosophila Stock CenterRRID:BDSC_7415
Genetic reagent (D. melanogaster)Act5C-Cas9Bloomington Drosophila Stock CenterRRID:BDSC_54590Act5C-Cas9.P
Genetic reagent (D. melanogaster)vGlutSS1Bloomington Drosophila Stock CenterRRID:BDSC_91246
Genetic reagent (D. melanogaster)brpd09839Bloomington Drosophila Stock CenterRRID:BDSC_85508
Genetic reagent (D. melanogaster)EcRM554fsBloomington Drosophila Stock CenterRRID:BDSC_4894
Genetic reagent (D. simulans)Lhr1 (D. simulans)Brideau et al., 2006
Genetic reagent (D. melanogaster)Df(4)ED6380Bloomington Drosophila Stock CenterRRID:BDSC_602664
Recombinant DNA reagentpAC-U63-QtgRNA2.1-ubiGal80(DE)-His2AV (plasmid)This studyin Materials and methods
Recombinant DNA reagentpAC-U63-QtgRNA2.1-tubGal80(DE)-His2AV (plasmid)This studyin Materials and methods
Recombinant DNA reagentpAC-U63-QtgRNA2.1-tubGal80(DE)-SV40 (plasmid)This studyin Materials and methods
Recombinant DNA reagentpAC-U63-QtgRNA2.1-tubBFP(HA) (plasmid)This studyin Materials and methods
Recombinant DNA reagentpAC-U63-QtgRNA2.1-tub-miRFP680-T2A-HO1(HA) (plasmid)This studyin Materials and methods
Recombinant DNA reagentpAC-U63-QtgRNA2.1–8 R (plasmid)Koreman et al., 2021RRID:Addgene 170514
Recombinant DNA reagentpENTR221-tubP (plasmid)Chen et al., 2025
Recombinant DNA reagentpAPIC-PHCS (plasmid)Han et al., 2011
Recombinant DNA reagentpAC-U63-QtgRNA2.1-BR (plasmid)Koreman et al., 2021RRID:Addgene 170513
SoftwareFijihttps://fiji.sc/RRID:SCR_002285
SoftwareRhttps://www.r-project.org/RRID:SCR_001905
SoftwareAdobe PhotoshopAdobeRRID:SCR_014199
SoftwareAdobe IllustratorAdobeRRID:SCR_010279
Chemical compoundDAPI (4',6-Diamidino-2-Phenylindole)Life TechnologyRRID:622481:1000 dilution
Antibodyanti-Elav 7E8A10 (Rat monoclonal)Developmental Studies Hybridoma BankRRID:AB_5282181:50 dilution
Antibodyanti-Repo 8D12 (Mouse monoclonal)Developmental Studies Hybridoma BankRRID:AB_5284481:50 dilution
Antibodyanti-Brp nc82 (Mouse monoclonal)Developmental Studies Hybridoma BankRRID:AB_23148661:100 dilution
Antibodyanti-vGluT (Rabbit polyclonal)Chen et al., 20241:200 dilution
Antibodyanti-HA 12CA5 (mouse monoclonal)Sigma AldrichRoche 115838160011:100 dilution
Antibodyanti-HRP conjugated with Cy3 (goat polyclonal)Jackson ImmunoResearchRRID:AB_23389521:200 dilution
Antibodyanti-mouse secondary antibody conjugated with Cy5 (donkey polyclonal)Jackson ImmunoResearchRRID:AB_23408201:400 dilution
Antibodyanti-rabbit secondary antibody conjugated with Cy5 (donkey polyclonal)Jackson ImmunoResearchRRID:AB_23406071:400 dilution
Antibodyanti-rat secondary antibody conjugated with Cy5 (donkey polyclonal)Jackson ImmunoResearchRRID:AB_23406721:400 dilution
Commercial assay or kitT4 ligaseNew England Biolabs Inc.#M0202
Commercial assay or kitNEBuilder HiFi DNA Assembly Master MixNew England Biolabs Inc.#E2621

Additional files

MDAR checklist
https://cdn.elifesciences.org/articles/108453/elife-108453-mdarchecklist1-v1.docx
Supplementary file 1

gRNA target sequences.

https://cdn.elifesciences.org/articles/108453/elife-108453-supp1-v1.xlsx

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  1. Yifan Shen
  2. Ann T Yeung
  3. Payton Ditchfield
  4. Elizabeth Korn
  5. Rhiannon Clements
  6. Xinchen Chen
  7. Bei Wang
  8. Zixian Huang
  9. Michael Sheen
  10. Parker A Jarman
  11. Chun Han
(2026)
A genome-wide MAGIC kit for recombinase-independent mosaic analysis in Drosophila
eLife 14:RP108453.
https://doi.org/10.7554/eLife.108453.3