REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-Scaf	Stephane Noselli (Rousset et al., 2010)	N/A
Rabbit anti-GFP	Invitrogen	Cat # A11122; RRID: AB_221569
Chicken anti-GFP	Invitrogen	Cat # A10262; RRID: AB_2534023
Rabbit anti-dsRed	Takara	Cat # 632496; RRID: AB_10013483
Goat anti-Chicken IgG (H+L), secondary antibody, alexa fluor 488	Invitrogen	Cat # A-11039; RRID: AB_142924
Donkey anti-mouse IgG (H+L), secondary antibody, alexa fluor 546	Invitrogen	Cat # A-10036; RRID: AB_2534012
Goat anti-Rabbit IgG (H+L), secondary antibody, alexa fluor 488	Invitrogen	Cat # A- 11008; RRID: AB_143165
Chemicals, Peptides, and Recombinant Proteins
TRIzol	Invitrogen	Cat # 15596026
Trehalase from porcine kidney	Sigma	Cat # T8778
Brilliant Blue FCF	Wako Chemicals	Cat # 02712842
Graduated microcapillary tube	Sigma	Cat # P0549
Light Cycler 480 Probes Master	Roche	Cat # 04887301001
Chloroform	Sigma	Cat # 288306
2-propanol	Sigma	Cat # I9516
Triton X-100	Sigma	Cat # T8787
Vectashield mounting medium	Vector Labs	Cat # H-1000
20% Paraformaldehyde (formaldehyde) aqueous solution	Electron Microscopy Sciences	Cat # 15713
Sulforhodamine	Sigma	Cat # S1402
Indigo Carmine	VWR	Cat # 22537.138
Critical Commercial Assays
RNeasy Mini Kit	QIAGEN	Cat # 74104
Glucose (HK) kit	Sigma	Cat # GAHK20-1KT
Superscript III first strand synthesis system	Thermo Fisher	Cat # 18080051
Deposited Data
RNA Sequencing reads	This paper	GEO: GSE107258
Experimental Models: Organisms/Strains
D. melanogaster, UAS-scaf	Stephane Noselli (Rousset et al., 2010)	N/A
D. melanogaster, Scaf protein trap line	DGRC Stock center, Kyoto Institute of Technology	DGRC stock # 109979
D. melanogaster, R50H04-GAL4	Bloomington Stock Center	Bloomington stock #46004
D. melanogaster, UAS-scaf-RNAi	Bloomington Stock Center	Bloomington stock # 55695
D. melanogaster, n-syb-GAL4	Bloomington Stock Center	Bloomington stock # 51635
D. melanogaster, UAS-mCD8::GFP	Bloomington Stock Center	Bloomington stock # 5137
D. melanogaster, UAS-DenMark-RFP	Nicolaï et al., 2010	N/A
D. melanogaster, UAS-GFP-Syd-1	Owald et al., 2010	N/A
D. melanogaster, UAS-dTrpA1	Hamada et al., 2008	N/A
D. melanogaster, UAS-TNT	Sweeney et al., 1995	N/A
D. melanogaster, tubP-GAL80ts	McGuire et al., 2003	N/A
Oligonucleotides
Primers for qRT-PCR	This paper	Table S3
Software and Algorithms
Trimmomatic	Bolger et al., 2014	http://www.usadellab.org/cms/?page=trimmomatic
Tophat2	Kim et al., 2013	https://ccb.jhu.edu/software/tophat/index.shtml
Cufflinks	Trapnell et al., 2012	http://cole-trapnell-lab.github.io/cufflinks/