REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Goat anti 5-HT	Immunostar	20079; RRID:AB_572262
Rat anti 5-HT	Millipore	MAB352; RRID:AB_11213564
Mouse anti CaMKIIα	Cell Signaling Technology	50049; RRID:AB_2721906
Rat anti CD31	BD Biosciences	550274; RRID:AB_393571
Rat anti CD68	AbD Serotec	MCA1957GA; RRID:AB_324217
Goat anti ChAT	Millipore	AB144P; RRID:AB_207951
Rabbit anti Collagen I	Abcam	ab21286; RRID:AB_446161
Rabbit anti Collagen III	Abcam	ab7778; RRID:AB_306066
Rabbit anti Collagen IV	AbD Serotec	2150-1470; RRID:AB_2082660
Goat anti Collagen IV	Southern Biotech	1340-01; RRID:AB_2721907
Goat anti Collagen VI	Southern Biotech	1360-01; RRID:AB_2721908
Rabbit anti Collagen VI	Abcam	ab6588; RRID:AB_305585
Mouse anti mu Crystallin	Abcam	ab54669; RRID:AB_943673
Rat anti Ctip2	Abcam	ab18465; RRID:AB_2064130
Rabbit anti Cux1	Santa Cruz Biotechnology	sc-13024; RRID:AB_2261231
Rabbit anti ER81	Santa Cruz Biotechnology	sc-28681; RRID:AB_2100826
Rabbit anti Fibronectin	Sigma-Aldrich	F3648; RRID:AB_476976
Mouse anti GFAP (Cy3 conjugated)	Sigma-Aldrich	C9205; RRID:AB_476889
Chicken anti GFAP	Millipore	AB5541; RRID:AB_177521
Guinea pig anti GFAP	Synaptic Systems	173 004; RRID:AB_10641162
Goat anti GFP (FITC conjugated)	Abcam	ab6662; RRID:AB_305635
Chicken anti GFP	Aves Labs	GFP-1020; RRID:AB_10000240
Rabbit anti GluR2/3	Millipore	AB1506; RRID:AB_90710
Guinea pig anti vGlut1	Millipore	AB5905; RRID:AB_2301751
Guinea pig anti vGlut2	Millipore	AB2251; RRID:AB_1587626
Mouse anti NeuN	Millipore	MAB377; RRID:AB_2298772
Guinea pig anti NeuN	Millipore	ABN90; RRID:AB_11205592
Chicken anti NF-H	Millipore	AB5539; RRID:AB_177520
Rabbit anti NG2	Millipore	AB5320; RRID: AB_91789
Rabbit anti P0	Abcam	ab31851; RRID:AB_2144668
Rabbit anti PDGFRα	Cell Signaling Technology	3164S; RRID:AB_10694389
Goat anti PDGFRα	R&D Systems	AF1062; RRID:AB_2236897
Rabbit anti PDGFRβ	Abcam	ab32570; RRID:AB_777165
Goat anti Podocalyxin	R&D Systems	AF1556; RRID:AB_354858
Rabbit anti S100	DAKO	Z0311; RRID:AB_10013383
Mouse anti Synapsin I	Synaptic Systems	106011; RRID:AB_2619772
Rabbit anti Synapsin I	Millipore	AB1543P; RRID:AB_90757
Mouse anti Synaptophysin	Abcam	ab8049; RRID:AB_2198854
Rabbit anti UCHL1	Abcam	ab10404; RRID:AB_297145
Guinea pig anti UCHL1	Abcam	ab10410; RRID:AB_297150
Streptavidin Cy3	Jackson Immunoresearch	016-160-084; RRID:AB_2337244
Streptavidin Alexa Fluor 594	Jackson Immunoresearch	016-580-084: RRID:AB_2337250
Streptavidin Alexa Fluor 647	Jackson Immunoresearch	016-600-084; RRID:AB_2337251
Donkey anti mouse biotin-SP (long spacer)	Jackson Immunoresearch	715-066-151; RRID:AB_2340788
Donkey anti rabbit biotin-SP (long spacer)	Jackson Immunoresearch	711-066-152; RRID:AB_2340594
Donkey anti rat Cy3	Jackson Immunoresearch	712-166-153; RRID:AB_2340669
Donkey anti rat Alexa Fluor 594	Jackson Immunoresearch	712-586-153; RRID:AB_2340691
Donkey anti rat Alexa Fluor 647	Jackson Immunoresearch	712-606-153; RRID:AB_2340696
Donkey anti mouse Alexa Fluor 488	Jackson Immunoresearch	715-546-151; RRID:AB_2340850
Donkey anti mouse Cy3	Jackson Immunoresearch	715-166-151; RRID:AB_2340817
Donkey anti mouse Alexa Fluor 647	Jackson Immunoresearch	715-606-151; RRID:AB_2340866
Donkey anti rabbit DyLight 405	Jackson Immunoresearch	711-476-152; RRID:AB_2632566
Donkey anti rabbit Alexa Fluor 488	Jackson Immunoresearch	711-546-152; RRID:AB_2340619
Donkey anti rabbit Cy3	Jackson Immunoresearch	711-166-152; RRID:AB_2313568
Donkey anti rabbit Alexa Fluor 647	Jackson Immunoresearch	711-606-152; RRID:AB_2340625
Donkey anti goat Alexa Fluor 488	Jackson Immunoresearch	705-546-147; RRID:AB_2340430
Donkey anti goat Cy3	Jackson Immunoresearch	705-166-147; RRID:AB_2340413
Donkey anti goat Alexa Fluor 647	Jackson Immunoresearch	705-606-147; RRID:AB_2340438
Donkey anti chicken DyLight 405	Jackson Immunoresearch	703-476-155; RRID:AB_2632562
Donkey anti chicken Alexa Fluor 488	Jackson Immunoresearch	703-546-155; RRID:AB_2340376
Donkey anti chicken Cy3	Jackson Immunoresearch	703-166-155; RRID:AB_2340364
Donkey anti chicken Alexa Fluor 647	Jackson Immunoresearch	703-606-155; RRID:AB_2340380
Donkey anti chicken A488	Jackson Immunoresearch	712-546-153; RRID:AB_2340686
Donkey anti chicken Cy3	Jackson Immunoresearch	712-166-153; RRID:AB_2340669
Donkey anti guinea pig DyLight 405	Jackson Immunoresearch	706-476-148; RRID:AB_2632564
Donkey anti guinea pig Alexa Fluor 488	Jackson Immunoresearch	706-546-148; RRID:AB_2340473
Donkey anti guinea pig Cy3	Jackson Immunoresearch	706-166-148; RRID:AB_2340461
Donkey anti guinea pig Alexa Fluor 647	Jackson Immunoresearch	706-606-148; RRID:AB_2340477
Mouse anti GAPDH	Millipore	MAB374; RRID:AB_2107445
Goat anti GFP	Abcam	ab6673; RRID:AB_305643
Rabbit anti HSP47	Acris	AP08508PU-N; RRID:AB_1954041
Rabbit anti P4HB	Abnova	PAB12587; RRID:AB_10556016
Rabbit anti PDGFRβ	Cell Signaling Technology	3169; RRID:AB_2162497
Rabbit anti Periostin	Abcam	ab14041; RRID:AB_2299859
Rabbit anti S100A4	Abcam	ab27957; RRID:AB_2183775
Donkey anti mouse HRP	Jackson ImmunoResearch	715-036-151; RRID:AB_2340774
Donkey anti rabbit HRP	Jackson ImmunoResearch	711-036-152; RRID:AB_2340590
Donkey anti goat HRP	Jackson ImmunoResearch	705-036-147; RRID:AB_2340392
Bacterial and Virus Strains
AAV9-CAG-ChR2-GFP	University of North Carolina Viral Vector Core (Dr. Ed Boyden)	N/A
AAV9-CAG-GFP	University of North Carolina Viral Vector Core (Dr. Ed Boyden)	N/A
Chemicals, Peptides, and Recombinant Proteins
4’6’-diamidino-2-phenylindole (DAPI)	Sigma-Aldrich	D9542
Tamoxifen	Sigma-Aldrich	T5648
Corn Oil	Sigma-Aldrich	C8267
Dextran, biotin, 10000MW, lysine fixable (BDA-10000)	Invitrogen	D1956
Vectashield antifade mounting medium	Vector Labs	H-1000
5-ethynyl-2′-deoxyuridine (EdU)	Molecular Probes	A10044
PhosSTOP Phosphatase Inhibitor Cocktail Tablets	Sigma-Aldrich (Roche)	PHOSS-RO ROCHE
cOmplete Protease Inhibitor Tablets	Sigma-Aldrich (Roche)	CO-RO ROCHE
Critical Commercial Assays
Click-iT EdU A647 imaging kit	Molecular Probes	C10340
A647 Antibody labeling kit	Molecular Probes	A20186
Mouse on mouse (MOM) basic kit	Vector Labs	BMK-2202
Pierce BCA protein assay kit	Thermo Scientific	23225
AllPrep DNA/RNA micro kit	QIAGEN	80284
SuperScript III first-strand synthesis system	Invitrogen	18080051
TaqMan universal master mix II	Applied Biosystems	4440040
Buffer RLT	QIAGEN	79216
AllPrep DNA/RNA/protein mini kit	QIAGEN	80004
Qubit RNA BR assay kit	Life Technologies	Q10210
Agilent RNA 6000 nano kit	Agilent Technologies	5067-1511
Deposited Data
Raw data files for RNA-seq	This paper	NCBI GEO: GSE93976
Mouse reference genome, mm9, NCBI Build 37	Mouse Genome Sequencing Consortium / NCBI	https://www.ncbi.nlm.nih.gov/grc/mouse
Experimental Models: Organisms/Strains
Mouse: Tg(Glast-CreERT2)	Slezak et al., 2007	N/A
Mouse: HRas–/–;NRas–/–; KRaslox/lox (Rasless)	Drosten et al., 2010	N/A
Mouse: B6.129X1-Gt(Rosa)26Sortm1(EYFP)Cos/J (R26R-YFP Cre reporter line)	The Jackson Laboratory	JAX:006148
Oligonucleotides
See Table S3	N/A	N/A
Software and Algorithms
Catwalk XT	Noldus Information Technology	N/A
Prism version 6.0g for Mac	GraphPad Software, Inc	N/A
ImageJ/Fiji version 2.0.-rc-43/1.51 g for Mac	Schindelin et al., 2012	N/A
QIAGEN’s Ingenuity Pathway Analysis (IPA)	QIAGEN	http://www.ingenuity.com
Database for Annotation, Visualization and Integrated Discovery (DAVID)	Huang et al., 2009a, Huang et al., 2009b	https://david.ncifcrf.gov/tools.jsp
TopHat version 1.3.3	Trapnell et al., 2009	N/A
Picard Tools version 1.29	Broad Institute, Cambridge, MA, USA	http://broadinstitute.github.io/picard
Cufflinks version 1.3.0	Trapnell et al., 2010	N/A
HTSeq version 0.5.1	Anders et al., 2015	N/A
R/Bioconductor package DSeq	Anders and Huber, 2010	N/A
MClust spike sorting toolbox version 1.0 for MATLAB	A David Redish	https://www.mathworks.com/matlabcentral/fileexchange/19311-mclust-spike-sorting-toolbox