| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-Delta ECD (1:2000) | DSHB | Cat# c594.9b; RRID: AB_528194 |
| Mouse anti-Notch ECD (1:100) | DSHB | Cat# c458.2h; RRID: AB_528408 |
| Mouse anti-Prospero (MR1A; 1:1000) | DSHB | RRID: AB_528440 |
| Chicken anti-GFP (1:2000) | Abcam | Cat# ab13970; RRID: AB_300798 |
| Goat anti-ßGAL (1:500) | Biogenesis | Cat# 466–1409 |
| Rabbit anti-Pdm1 (1:1000) | Gift from X. Yang, Zhejiang University, China |
RRID: AB_2570215 |
| Rabbit anti-PH3 (1:1000) Millipore | Millipore | Cat# 06-570; RRID: AB_310177 |
| Goat anti-Kismet DK20 (1:500) | Santa Cruz | sc-15848; RRID: AB_672122 |
| Rabbit anti-Utx, (1:500) | Gift from A. Shilatifard, Northwestern University Feinberg School of Medicine |
RRID: AB_2567973 |
| Rabbit anti-Trr (1:500) | Gift from A. Shilatifard, Northwestern University Feinberg School of Medicine |
RRID: AB_2568870 |
| Rabbit anti-Lpt (1:500) | Gift from A. Shilatifard, Northwestern University Feinberg School of Medicine |
RRID: AB_2568872 |
| Rabbit anti-H3K4me1 (1:500) | Gift from A. Shilatifard, Northwestern University Feinberg School of Medicine |
N/A |
| Rabbit anti-dpERK (1:200) | Cell Signaling Technology | Cat# 4377; RRID: AB_331775 |
| Rabbit anti-H3K27me3 (1:500) | Diagenode | Cat# C15410195; RRID: AB_2753161 |
| Rabbit anti-H3K27ac (1:2000) | Abcam | Cat# ab4729; RRID: AB_2118291 |
| Mouse anti-EGFR (1:100) | Sigma | Cat# E2906; RRID: AB_609900 |
| Rabbit anti-DH31 (1:500), | Gift from J.A. Veenstra, Université de Bordeaux |
RRID: AB_2569126 |
| Rabbit anti-LTK2 (1:1000) | Gift from J.A. Veenstra, Université de Bordeaux |
N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Alexa 647-conjugated phalloidin (1:100) | LifeTechnologies | Cat# A22287: RRID: AB_2620155 |
| Quick ligase | NEB | Cat# M2200S |
| RNase A | Sigma | Cat# R6513-50MG |
| T4 DNA ligase | NEB | Cat# B0202S |
| DpnI | NEB | Cat#R0176L |
| DpnII | NEB | Cat#R0543L |
| Sau3AI | NEB | Cat# R0169L |
| PCR buffer MyTaq HS | Bioline | Cat# BIO-21111 |
| AlwI | NEB | Cat# R0513S |
| Klenow fragment | NEB | Cat# 210S |
| T4 polynucleotide kinase | NEB | Cat# M0201S |
| Elastase | Sigma | Cat# E0258-5MG |
| Critical Commercial Assays | ||
| Qiaquick PCR Purification kit | Qiagen | Cat# 28104 |
| QIAmp DNA Micro Kit | Qiagen | Cat# 56304 |
| Arcturus PicoPure RNA Isolation Kit | ThermoScientific | Cat# KIT0202 |
| RNase-Free DNase Set | Qiagen | Cat# 79254 |
| Arcturus™ RiboAmp™ HS PLUS Kit | ThermoScientific | Cat# KIT0525 |
| Deposited Data | ||
| Lists of expressed genes and cell type-specific genes were generated from published RNAseq data in the gut | Dutta et al., 2015 | http://flygutseq.buchonlab.com/resources |
| Experimental Models: Organisms/Strains | ||
| Drosophila: FRT40A kis10D26 | This study, Institut Curie Paris. | N/A |
| Drosophila: UAS-LT3-NDam | Southall et al., 2013 | N/A |
| Drosophila: kis1 | Daubresse et al., 1999 | Cat# 431, RRID:BDSC_431 |
| Drosophila: UAS-kis-RNAi #36597 | BDSC, (Perkins et al., 2015) | Cat# 36597, RRID:BDSC_36597 |
| Drosophila: UAS-kismet RNAi #34908 | BDSC, (Perkins et al., 2015) | BDSC Cat# 34908, RRID:BDSC_34908) |
| Drosophila: UAS-EGFRDN | BDSC (Buff et al., 1998) | BDSC Cat# 5364, RRID:BDSC_5364 |
| Drosophila: UAS-lpt-RNAi | BDSC, (Perkins et al., 2015) | BDSC Cat# 25994, RRID:BDSC_25994 |
| Drosophila: UAS-trr-RNAi | BDSC, (Perkins et al., 2015) | BDSC Cat# 29563, RRID:BDSC_29563 |
| Drosophila: UAS-utx-RNAi | BDSC, (Perkins et al., 2015) | BDSC Cat# 34076, RRID:BDSC_34076 |
| Drosophila: FR82B trxE2 | BDSC (Gindhart and Kaufman, 1995) | BDSC Cat# 24160, RRID:BDSC_24160 |
| Drosophila: FR19A trrB | BDSC (Haelterman et al., 2014) | BDSC Cat# 57138, RRID:BDSC_57138 |
| Drosophila: UAS-bskDN | BDSC (Adachi-Yamada et al., 1999) | BDSC Cat# 6409, RRID:BDSC_6409 |
| Drosophila: UAS-yki-RNAi | BDSC, (Perkins et al., 2015) | BDSC Cat# 34067, RRID:BDSC_34067 |
| Drosophila: UAS-InRDN | Gift to BDSC by Exelixis, Inc. | BDSC Cat# 8253, RRID:BDSC_8253 |
| Drosophila: UAS-domeRNAi | BDSC, (Perkins et al., 2015) | BDSC Cat# 34618, RRID:BDSC_34618 |
| Drosophila: UAS-ash1-RNAi # 31050 | BDSC, (Perkins et al., 2015) | BDSC Cat# 31050, RRID:BDSC_31050 |
| Drosophila: UAS-ash1-RNAi # 36130 | BDSC, (Perkins et al., 2015) | BDSC Cat# 36130, RRID:BDSC_36130 |
| Drosophila: UAS-brm-RNAi | BDSC, (Perkins et al., 2015) | BDSC Cat# 31712, RRID:BDSC_31712 |
| Drosophila: UAS-Cbl-RNAi | BDSC, (Perkins et al., 2015) | BDSC Cat# 27500, RRID:BDSC_27500 |
| Drosophila: UAS-GFP-E2f1-230, UAS-mRFP-CycB1-266 | BDSC (Zielke et al., 2014) | BDSC Cat# 55118, RRID:BDSC_55118 |
| Drosophila: 10XSTAT92E-GFP | BDSC (Ekas et al., 2006) | BDSC Cat# 26198, RRID:BDSC_26198 |
| Drosophila: CycE-lacZ | BDSC Gift by Helena Richardson, Peter MacCallum Cancer Centre to BDSC |
BDSC Cat# 30722, RRID:BDSC_30722 |
| Drosophila: UAS-set1-RNAi | VDRC, (Dietzl et al., 2007) | Cat# 40682 |
| Drosophila: UAS-cic-RNAi | VDRC, (Dietzl et al., 2007) | Cat# 103805 |
| Drosophila: FRT40A kisLM27 | Gift from D.R. Marenda, Drexel University. |
N/A |
| Drosophila: FRT40A kisEC1 | Gift from D.R. Marenda | N/A |
| Drosophila: NRE-LacZ | Furriols and Bray, 2001 | N/A |
| Drosophila: UAS-Notchcdc10 | Brennan et al., 1999 | N/A |
| Drosophila: UAS-LT3-NDam-RNAPol II | Southall et al., 2013 | N/A |
| Drosophila: UAS-LT3-Dam-Pc | Marshall and Brand, 2017 | N/A |
| Drosophila: UAS-LT3-Dam-HP1a | Marshall and Brand, 2017 | N/A |
| Drosophila: UAS-LT3-Dam-Brm | Marshall and Brand, 2017 | N/A |
| Drosophila: UAS-LT3-Dam-H1 | Marshall and Brand, 2017 | N/A |
| Drosophila: UAS-cicHA | Jin et al., 2015 | N/A |
| Drosophila: pucE69-LacZ | Gift from N.Tapon, Francis Crick Institute, London | N/A |
| Drosophila: Upd-LacZ | Gift from B.A. Edgar, Huntsman Cancer Institute, Utah |
N/A |
| Drosophila: Upd3.1-LacZ | Gift from B.A. Edgar, Huntsman Cancer Institute, Utah |
N/A |
| Drosophila: UAS-Cbl-L | Gift from L.M. Pai, Chang Gung University, Taiwan |
N/A |
| Drosophila: UAS-Cbl-S | Gift from L.M. Pai, Chang Gung University, Taiwan |
N/A |
| Drosophila: NRE-GAL4 ; tubGAL80ts UAS-GFP | Zeng et al., 2010 | N/A |
| Drosophila: esg-GAL4, tubGAL80ts UAS-GFP | Jiang et al., 2009 | N/A |
| Drosophila: esg-GAL4 UAS-GFP; Su(H)GBE-GAL80 tubGAL80ts | Wang et al., 2014 | N/A |
| Drosophila: MyoIAGAL4; tubGAL80ts UAS-GFP | Jiang et al., 2009 | N/A |
| Drosophila: prosvoila-Gal4, tub-Gal80ts | Balakireva et al., 1998 | N/A |
| Drosophila: w P[hs-FLP] P[pTub-GAL4] P[UAS-nlsGFP] | Bardin et al., 2010 | N/A |
| Drosophila: FRT40A P[pTub-GAL80] | Bardin et al., 2010 | N/A |
| Drosophila: FRT82B P[pTub-GAL80] | Bardin et al., 2010 | N/A |
| Drosophila: w P[hs-FLP]; FRT40A P[pTub-GAL80]; Drosophila: P[UAS-RFP], P[pTub-GAL4] | This paper, Institut Curie, Paris. | N/A |
| Drosophila: hsflp122 P[pTub-GAL80] FRT19A; P[pAct-GAL4] P[UASGFP] | Lin et al., 2008 | N/A |
| Recombinant DNA | ||
| Drosophila BAC: (P[acman] BAC CH322-128O7) | BACPAC Resources Center | CH322-128O7 |
| Drosophila BAC: (P[acman] BAC CH321-35E09) | BACPAC Resources Center | CH321-35E9 |
| Plasmid: kislocus-FLP | This paper, Institut Curie, Paris. | N/A |
| Plasmid: R6kam-hNGFP | Gift from A. A. Hyman, Max Planck Institute, Dresden. |
N/A |
| Plasmid: UAS- KisS-Flag | This paper, Institut Curie, Paris. | N/A |
| Plasmid: UAS-KisL-His-Flag | This paper, Institut Curie, Paris. | N/A |
| Plasmid: UAS-kis-K2060R-His-Flag | This paper, Institut Curie, Paris. | N/A |
| Plasmid: pUASTattB-LT3-NDam | Southall et al., 2013 | N/A |
| Plasmid: UAS-LT3-Dam-Kis | This paper, Institut Curie, Paris. | N/A |
| Plasmid: UAS-LT3-Dam-Trr | This paper, Institut Curie, Paris. | N/A |
| Software and Algorithms | ||
| Prism 7 | GraphPad Software | RRID:SCR_002798 |
| FIJI | https://fiji.sc | N/A |
| Damidseq_pipeline | Marshall and Brand, 2015 | https://owenjm.github.io/ |
| bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| bedtools | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/index.html |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| deepTools plotHeatmap | Ramírez et al., 2014 | https://deeptools.readthedocs.io/en/develop/content/tools/plotHeatmap.html |
| polii.gene.call | Marshall and Brand, 2015 | https://owenjm.github.io/ |
| Galaxy | Afgan et al., 2016 | https://usegalaxy.org |
| IPython | https://ipython.org | |
| Galaxy workflow | IPython notebooks and UMAP code used in this study - Institut Curie Paris | https://github.com/bardin-lab/kismet-analysis |
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