A cell-type-specific alternative splicing regulator shapes synapse properties in a trans-synaptic manner

. 2023 Mar 1;42(3):112173. doi: 10.1016/j.celrep.2023.112173

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies

Rabbit anti-SAM68	Iijima et al.³⁵	N/A
Rabbit anti-SLM2	Iijima et al.³⁵	N/A
Guinea pig polyclonal anti-SLM2	Iijima et al.³⁵	N/A
Mouse anti-NeuN	Chemicon	#MAB377
Rat anti-HA monoclonal clone 3F10	Roche	#11867431001
Rabbit anti-Ctip2 polyclonal	Novus Biological	#NB100-2600
Donkey anti-guinea pig IgG Cy5-conjugated	Jackson ImmunoResearch	#706-175-148
Donkey anti-rabbit IgG Cy3-conjugated	Jackson ImmunoResearch	#711-165-152
Donkey anti-guinea pig IgG Cy3-conjugated	Jackson ImmunoResearch	#706-165-148
Donkey anti-rabbit IgG Alexa 488-conjugated	Thermo Fisher	#A-21206

Chemicals, peptides, and recombinant proteins

anti-HA magnetic beads clone 2–2.2.14	Thermo Fisher/Pierce	#88836
Complete mini Protease Inhibitors, EDTA-free	Roche	#04693159001
RNAsin	Promega	#N2115
Cycloheximide	Sigma	#C7698
Heparin	Sigma	#H3393
IGEPAL-CA640 (NP-40)	Sigma	#18896
RNeasy Micro plus kit	Qiagen	#74034
Dynabeads™ Protein A	Invitrogen	#10001D
TURBO™ DNase (2 U/ul)	Invitrogen	#AM2238
Ambion™ RNase I (100 U/ul)	Invitrogen	#AM2295
T4 PNK (10 U/ul)	NEB	#M0314L
T4 RNA Ligase 1 (ssRNA Ligase), High Concentration	NEB	#M0437M
Proteinase K, Molecular Biology Grade (0.8 U/ul)	NEB	#P8107S
Q5® High-Fidelity 2X Master Mix	NEB	#M0492S
ExoSAP-IT™	Applied Biosystems	#78200.200.UL
SuperScript™ III Reverse Transcriptase	Invitrogen	#18080093
Dynabeads™ MyOne™ Silane	Invitrogen	#37002D
NuPAGE™ Transfer Buffer (20X)	Invitrogen	#NP0006
NuPAGE™ 4–12%, Bis-Tris, 1.5 mm, Mini Protein Gels	Invitrogen	#NP0335BOX
NuPAGE™ MOPS SDS Running Buffer (20X)	Invitrogen	#NP0001
Amersham™ Protran® Western blotting membranes, nitrocellulose	Sigma	#GE10600002
RNA Clean & Concentrator-5	Zymo Research	#R1015
Acid-Phenol:Chloroform, pH 4.5	Invitrogen	#AM9720
Phase Lock Gel™ Heavy tubes	5 PRIME	#2302830
Urea for molecular biology	AppliChem	#A1049
Prolong Diamond Antifade Mountant	Life Technologies	#P36970
Dako Fluorescence Mounting medium	Agilent	#S3023
OCT	Tissue-Tek

Critical commercial assays

HiSeq SBS Kit v4	Illumina	#FC-401-4003
NGS Fragment Analysis Kit	Advanced Analytica	#DNF-473
RNA 6000 Pico Chip	Agilent	#5067–1513
QuantiFluor RNA System	Promega	#E3310

Deposited data

RNA-seq data	This paper	GEO: GSE209870
CLIP-seq data	This paper	GEO: GSE220062
RNA-seq data Sam68^KO	Witte et al.⁶⁶	PRIDE: PRJEB27529
RNA-seq data Slm2^KO	Traunmüller et al.³⁷	GEO: GSE79902

Experimental models: Organisms/strains

Mouse: C57BL/6J	Janvier	N/A
Mouse: Grik4-cre	Jackson Laboratories	strain #:006,474
Mouse: Camk2a-cre	Jackson Laboratories	strain #:005,359
Mouse: Sst-IRES-Cre	Jackson Laboratories	strain #:013,044
Mouse: Ai32 ROSA-stop-ChR2/H134R	Jackson Laboratories	strain #:024,109
Mouse: Slm2/KHDRBS3 flox	Traunmüller et al.³⁶	N/A
Mouse: Ai9 ROSA-stop-tomato	Jackson Laboratories	strain #:007,909
Mouse: RjOrl:SWISS	Janvier	N/A
Mouse: Rpl22-HA	Jackson Laboratories	strain #:029,977

Oligonucletides

For oligonucleotides, see Table S3	N/A	N/A

Software and algorithms

Fiji	Traunmüller et al.⁶⁷	RRID:SCR_002285
FeatureCounts	Liao et al.⁶⁸	RRID:SCR_012919
CTK	Shah et al.⁴²	RRID:SCR_019034
mCross	Feng et al.⁴⁴	N/A
FastQC 0.11.8	N/A	RRID:SCR_014583
Picard v1.119	N/A	RRID:SCR_006525
RSeQC v2.3.9	N/A	RRID:SCR_005275
SAMTOOLS 1.13	Li et al.⁶⁹	RRID:SCR_002105
STAR 2.7.9a	Dobin et al.⁷⁰	RRID:SCR_004463
DESEQ2	Love et al.⁷¹	RRID:SCR_015687
CLIPper 2.0.0	Yeo et al.⁷²	https://github.com/YeoLab/clipper
IDR 2.0.3	Li et al.⁷³	RRID:SCR_017237
Sashimi.py	Zhang et al.⁷⁴	https://github.com/ygidtu/sashimi.py
DAVID	Huang et al.⁷⁵	RRID:SCR_001881
SynGO	Koopmans et al.⁴⁵	RRID:SCR_017330
Ethovision10	Noldus	N/A
Stimfit	Guzman et al.⁷⁶	RRID:SCR_016050
pyABF	N/A	http://swharden.com/pyabf
Imaris 7.0.0	Bitplane AG	RRID:SCR_007370
Cutadapt 3.4	N/A	RRID:SCR_011841
UMI-tools 1.1.1	Smith et al.⁷⁷	RRID:SCR_017048