REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Vidisic eye gel	Bausch and Lomb	N/A
Iodobromine/ Braunoderm	Braun	Cat#3881105
Fast Green	Sigma	Cat#F7252
TEMGESIC 0.3 mg (buprenorphine)	Indivior Europe Ltd. Dublin, Ireland	Cat#00345928
Metacam (Meloxicam)	Boehringer Ingelheim	Cat#158669-002
Isoflurane Baxter vet	Baxter	Cat#HDG9623V
DPBS, no calcium, no magnesium	Invitrogen	Cat#14190094
Hibernate-E medium	Thermo Fisher Scientific	Cat#A1247601
HBSS	Invitrogen	Cat#14170088
Papain	Sigma	Cat#P4762
DNaseI	Sigma	Cat#D4263
FCS	Biochrom	Cat#S0115
DMEM	Invitrogen	Cat#6196526
Trypan blue	Invitrogen	Cat#15090046
Hoechst dye	Invitrogen	Cat#33258; RRID: AB2651133
Triethyl ammonium bromide (TEAB)	Sigma-Aldrich	Cat#241059
Sodium deoxycholate (SDC)	Sigma-Aldrich	Cat#30970
Dithiothreitol (DTT)	Sigma-Aldrich-Merck	Cat#DTT-RO
Iodoacetamide (IAA)	Sigma-Aldrich	Cat#I1149
Powdered trypsin (sequencing grade modified trypsin)	Promega	Cat#V5111
Pierce HeLa protein digest standard	Thermo Fisher Scientific	Cat#88328
Formic acid (FA)	Promega	Cat#F0507-100ML
Hydroxylamine	Sigma-Aldrich	Cat#438227
Ammonium bicarbonate	Sigma-Aldrich	Cat#A6141
Acetonitrile	Sigma-Aldrich-Merck	Cat#271004-100ML
Critical commercial assays
QIAGEN Endo-Free Maxi Prep Kit	QIAGEN	Cat#12362
TMT10plex Reagent Set for Isobar Marking	Thermo Fisher Scientific	Cat#90110
RNeasy Micro Kit (50)	QIAGEN	Cat#74004
Eukaryote Total RNA Pico assay	Agilent	Cat#5067-1513
SMART-Seq v4 Ultra Low Input RNA Kit	Clontech Laboratories	Cat#634891
Nextera XT DNA Library Preparation Kit	Illumina	Cat#FC-131-1096
Experimental models: Organisms/strains
Mice; C57BL/6J; both sexes, preferentially < one year old	Charles River	https://www.bionity.com/en/companies/24848/charles-river-germany-gmbh-co-kg.html; Strain #: 632
Recombinant DNA
pSilencer2-U6-shControl	Xie et al.18	N/A
pSilencer2-U6-shCep120	Xie et al.18	N/A
pCAG-tDimer	A gift from Thomas Oertner	N/A
pCAG-Venus	A gift from Phil Sharp; (de Anda et al., 201019)	RRID: Addgene_127346
pGLAST-dsRed2	A gift from Nicholas Gaiano (via Addgene); (Mizutani et al.)16	RRID: Addgene_17706
pNeuroD-ires-eGFP	A gift from Zhigang Xie; (de Anda et al., 201019) and via Addgene	RRID:Addgene_61403
Software and algorithms
Human Reviewed FASTA Database	UniProt	N/A
SEQUEST algorithm integrated into Proteome Discoverer 2.4	Thermo Fisher Scientific	https://www.thermofisher.com/de/de/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html
R software environment	R Core Team, 2022	https://cran.r-project.org/
rstatix (CRAN R package)	Kassambara, 202120	https://cran.r-project.org/web/packages/rstatix/index.html
ggplot2 (CRAN R package)	Warnes et al., 202221	https://cran.r-project.org/web/packages/gplots/index.html
dendextend (CRAN R package)	Galili, 201522	https://cran.r-project.org/web/packages/dendextend/index.html
DESeq2 v. 1.43.0 (Bioconductor R package)	Love et al., 201423	https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
clusterProfiler (Bioconductor R package)	Wu et al., 202124	https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
STRING	Szklarczyk et al., 201925	https://string-db.org/
WebGestalt	Liao et al., 201926	http://www.webgestalt.org
ComplexHeatmap v. 2.14.0	Gu et al., 201627	https://doi.org/10.1093/bioinformatics/btw313
dplyr v. 1.0.10	Wickham, 201928	https://dplyr.tidyverse.org
mixOmics v. 6.17.12	Rohart et al., 201729	https://CRAN.R-project.org/package=mixOmics
tidyverse 1.3.2	Wickham, 201928	https://doi.org/10.21105/joss.01686
BD FACSDiva software	BD Biosciences	https://www.bdbiosciences.com/en-us/products/software/instrument-software/bd-facsdiva-software
FlowJo	BD Biosciences	https://www.bdbiosciences.com/en-us/products/software/flowjo-v10-software
Other
Mouse food powder	Altromin	Cat#1311P
Mouse biohuts made of tinted transparent polycarbonate	Tecniplast	N/A
Graefe forceps	Fine Science Tools	11049-10
Gross anatomy probe	Fine Science Tools	10088-15
Micropipette puller	Flaming/Brown MP puller, Sutter Instrument Co.	Model P-97
NanoDrop	Thermo Fisher Scientific	https://www.thermofisher.com/de/de/home/industrial/spectroscopy-elemental-isotope-analysis/molecular-spectroscopy/uv-vis-spectrophotometry/instruments/nanodrop/instruments.html#nanodrop-eight
Borosilicated micropipettes	Science Products GmbH	Cat#GB100TF
Isoflurane-O2 mixer device, Dräger Vaporizer 19.1	Drägerwerk AG	N/A
Fluovac	Harvard Apparatus	N/A
Isoflurane adsorber	Stoelting	Cat#50207
Double edge PERSONNA coated razor blades	Electron Microscopy Sciences	Cat#72000
Ring forceps – 9 cm	Fine Science Tools	Cat#11106-09
Standard pattern forceps – serrated straight 14 cm	Fine Science Tools	Cat#11000-14
Strabismus scissors – straight blunt 9 cm	Fine Science Tools	Cat#14074-09
Kelly hemostat – serrated straight 14 cm	Fine Science Tools	Cat#13019-14
Forceps – serrated straight 7cm	Fine Science Tools	Cat#11064-07
Dumont #5 mirror finish forceps	Fine Science Tools	Cat#11252-23
Extra thin Iris scissors – straight 10.5 cm	Fine Science Tools	Cat#14088-10
Extra fine Iris scissors – curved 8.5 cm	Fine Science Tools	Cat#14085-08
Strabismus scissors straight blunt 9 cm	Fine Science Tools	Cat#14074-0908
Surgical scissors Mayo-Stille – 17 cm	Fine Science Tools	Cat#14012-17
Alcohol pads	Braun	Cat#9160612
Platinum tweezer electrode 5 mm	Harvard Apparatus	Cat#EC1 45-0489
Electroporator ECM 830 BTX and BTX generator footswitch (model 1250FS)	Harvard Apparatus	Cat#EC1 45-0052
Vicryl thread	Ethicon	Cat#V994H
Silk thread	Silkam	Cat#C0762130
Stereo microscope model SZX16	Olympus	https://www.olympus-ims.com/en/microscope/szx16/
BD FACS AriaIIIu	BD Biosciences	N/A
BD FACS AriaFusion	BD Biosciences	N/A
ThermoMix C	Eppendorf, Germany	Cat#5382000015
Probe sonicator	N/A	N/A
SpeedVac SC110 Savant	Thermo Fisher Scientific	N/A
Monolith column ProSwift RP-4H, 1 mm × 250 mm	Thermo Fisher Scientific	Cat#164921
Agilent 1200 series HPLC monolith column ProSwift RP-4H, 1 mm × 250 mm	Agilent Technologies Thermo Fisher Scientific	https://www.agilent.com/en/products/liquid-chromatography
RP fractionation column Agilent 1200 series HPLC	Agilent Technologies	https://www.agilent.com/en/products/liquid-chromatography
Dionex Ultimate 3000 UPLC	Thermo Fisher Scientific	https://www.thermofisher.com/de/de/home/industrial/chromatography/liquid-chromatography-lc/hplc-uhplc-systems
Acclaim PepMap 100, 75 μm × 50 cm, 100 Å pore size , 2 μm particle size	Thermo Fisher Scientific	Cat#164564
Orbitrap Fusion	Thermo Fisher Scientific	https://www.thermofisher.com/de/de/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-systems
7900HT fast real-time PCR system	Thermo Fisher Scientific	Cat#4329001
2100 Bioanalyzer instrument	Agilent	Model G2939B
Illumina NextSeq 550 platform	Illumina	https://emea.illumina.com/systems/sequencing-platforms/nextseq.html