REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-Futsch (clone 22C10)	DSHB (University of Iowa)	RRID: AB_528403
Anti-Digoxigenin-POD, Fab fragments	Roche	Cat. 11207733910; RRID: AB_514500
Anti-Fluorescein-POD	Roche	Cat. 11426320001; RRID: AB_514503
Biotin Monoclonal Antibody (clone Z021) HRP	Thermo Fisher Scientific	Cat. 03-3720; RRID: AB_2522266
Chemicals, Peptides, and Recombinant Proteins
T7 RNA polymerase	Roche	10881767001
SP6 RNA polymerase	Roche	10810274001
DIG labeling mix	Roche	11277073910
Biotin RNA Labeling Mix	Roche	11685597910
Fluorescein RNA Labeling Mix	Roche	11685619910
Western Blocking Reagent Solution	Roche	11921673001
Critical Commercial Assays
NEBNext Ultra Directional RNA Library Prep Kit for Illumina	NEB	E7420
TSA-Plus Cy3 and Fluor	Perkin Elmer	NEL753001KT
Deposited Data
Raw sequencing data twi::EGFP-CBP20 line (RNaseq)	This paper	ArrayExpress: E-MTAB-4069
Raw sequencing data twi::EGFP-CBP20 line (CAGE)	This paper	ArrayExpress: E-MTAB-4070
Raw sequencing data vas::Cas9 and KO lines (RNaseq)	This paper	ENA: ERP110650
Drosophila melanogaster reference genome, R5/dm3	Berkeley Drosophila Genome Project	http://www.fruitfly.org/sequence/release5genomic.shtml
Drosophila melanogaster genome annotation, R5.55	FlyBase	ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/
Genomic coordinates of novel lncRNA genes	This paper	http://furlonglab.embl.de/data/
Experimental Models: Organisms/Strains
D. melanogaster: twi::EGFP-CBP20 line: w[1118];;P{twi::ECFP-CBP20,w[+mC] }	This paper	N/A
D. melanogaster: vas::Cas9 line: w[1118]; PBac{y[+mDint2] = vas-Cas9}VK00027	Bloomington Drosophila Stock Center	BDSC: 51324
Oligonucleotides
Primers for FISH probe amplification by PCR	See Table S6	N/A
Primers for qPCR	See Table S6	N/A
Software and Algorithms
STAR v2.3.1z	[68]	https://github.com/alexdobin/STAR/releases
Trinity release 2014-07-17	[69]	https://github.com/trinityrnaseq/trinityrnaseq/releases
GMAP version 2013-03-31	[70]	http://research-pub.gene.com/gmap/
Cufflinks v2.1.1	[71]	https://github.com/cole-trapnell-lab/cufflinks
DEseq2 v1.2.10	[72]	https://bioconductor.org/packages/release/bioc/html/DESeq2.html