Antibodies |
|
V5 Tag Monoclonal Antibody |
Invitrogen |
Cat# R96025
|
Rabbit Anti-V5 Antibody |
Novus |
Cat# NB600-381 |
β-Tubulin (9F3) Rabbit mAb |
Cell Signaling Technologies |
Cat# 2128 |
Anti-c-Myc Antibody (Clone #9E10) |
Sigma-Aldrich |
Cat# M4439 |
Rabbit Anti-HA Antibody |
Sigma-Aldrich |
Cat# H6908 |
Anti-Tubulin Beta 3 (TUBB3) Antibody-Cy5 conjugated |
Biolegend |
Cat# 6S7406; RRID: AB_2563610 |
Anti-Isl ½ Antibody |
Developmental Studies Hybridoma Bank |
Cat# 39.4DS; RRID: AB_2314683 |
Anti AcetylCholine Transferase Antibody |
Sigma-Aldrich |
Cat# AB144P |
MAP2 Polyclonal Antibody |
Proteintech |
Cat# 17490-1-AP |
Human/Mouse/Rat Sox2 Antibody (Clone #245610) |
R & D Systems |
Cat# MAB2018 |
Human Oct4 Antibody (Clone #653108) |
R & D Systems |
Cat# MAB17591 |
Anti-Kif5A Antibody |
Genetex |
Cat# GTX113761; RRID: AB_2037309 |
RBM24 Polyclonal Antibody |
Invitrogen |
Cat# PAS-66881 |
Rabbit Anti-RAN Antibody |
Bethyl Laboratories |
Cat# A304-297A |
Anti-mutKif5A Antibody |
This paper, Genewiz |
N/A |
Anti-GAPDH Antibody |
Novus Biologicals |
Cat# NB300-327 |
Rabbit Anti-HA Tag Antibody |
Sigma-Aldrich |
Cat# H6908 |
Goat Anti-Horseradish Peroxidase Antibody |
Jackson Immunoresearch |
Cat# 123-165-021; RRID: AB_2338959 |
Donkey Anti-Mouse 488 |
Jackson Immunoresearch |
RRID: AB_2340846 |
Donkey Anti-Rabbit IgG 647 |
Jackson Immunoresearch |
RRID: AB_2492288 |
Donkey Anti-Rabbit IgG 594 |
Jackson Immunoresearch |
RRID: AB_2340621 |
Donkey anti-Mouse 546 |
Invitrogen |
Cat# A10036 |
Mouse anti-Hemagglutinin (HA) antibody (12CA5) |
Invitrogen |
Cat# MA1-12429; RRID: AB_1074049 |
Goat anti-Mouse FITC |
Jackson Immunoresearch |
Cat# 115-095-003; RRID: AB_2338589 |
Goat anti-Mouse TRITC |
Jackson Immunoresearch |
Cat#115-025-003; RRID: AB_2338478 |
Rabbit anti-GFP |
Proteintech |
Cat# 50430-2-AP |
Goat anti-Mouse HRP |
Jackson Immunoresearch |
Cat# 115-035-003; RRID: AB_10015289 |
Goat anti-Rabbit HRP |
Jackson Immunoresearch |
Cat# 111-004-003; RRID: AB_2337913 |
|
Biological samples |
|
Patient Kif5A iPSC |
Applied Stem Cell; This paper |
N/A |
Isogenic Control iPSC |
Applied Stem Cell |
ASE-9109 |
|
Chemicals, peptides, and recombinant proteins |
|
FuGENE6 transfection reagent |
Promega |
Cat# E269A |
Tetramethylrhodamine (TMR) Halo ligand |
Promega |
Cat# G8251 |
Guanosine-5’-[(α,β)-methyleno] triphosphate, sodium salt (GMPCPP) |
Jena Bioscience |
Cat# NU-405 |
Porcine brain tubulin |
Cytoskeleton |
Cat# T240 |
HiLyte488-labeled tubulin |
Cytoskeleton |
Cat# TL488M |
Purified Rigor Kinesin |
Masucci et al. (2021)
|
N/A |
PlusOne Repel-Silane ES |
Cytiva |
Cat# 17133201 |
Pluronic F-127 |
Sigma-Aldrich |
Cat# P2443 |
Methyl cellulose |
Sigma-Aldrich |
Cat# M0512 |
Adenosine 5’-triphosphate magnesium salt (ATP) |
Sigma-Aldrich |
Cat# A9187 |
Guanosine 5’-triphosphate sodium salt hydrate (GTP) |
Sigma-Aldrich |
Cat# G8877 |
0.05% Trypsin EDTA |
Gibco |
Cat# 25300054 |
Poly-D-Lysine |
Sigma-Aldrich |
Cat# P7280-5X5MG |
Natural Mouse Laminin |
Corning |
Cat# 354232 |
Neurobasal Medium, Minus Phenol Red |
Gibco |
Cat# 12348-017 |
B27 Supplement |
Gibco |
Cat# 17504-044 |
Glutamax |
Gibco |
Cat# 35050061 |
Opti-MEM I Reduced Serum Medium, no phenol red |
Gibco |
Cat# 11058021 |
Lipofectamine 2000 Transfection Reagent |
Invitrogen |
Cat# 11668019 |
2-Mercaptoethanol, 99% pure |
Fisher Scientific |
Cat# AC125470100 |
Dulbecco’s Modified Eagle Medium (DMEM) |
Gibco |
Cat# 11965118 |
Fetal Bovine Serum, Regular |
MediaTech |
Cat# 35-010-CV |
L-glutamine (200 mM) |
Gibco |
Cat# 25030081 |
Penicillin/Streptomycin |
Gibco |
Cat# 15140122 |
NeuroMag Transfection Reagent |
Oz Biosciences |
Cat# NM50200 |
Minimum Essential Media (MEM) |
Gibco |
Cat# 11095098 |
BSA (heat shock fraction, protease free) |
Sigma-Aldrich |
Cat# A3294 |
Triton X- |
Sigma-Aldrich |
Cat# T9284 |
Antigen Retrieval Buffer |
Abcam |
Cat# 93678 |
Prolong Gold Antifade Mountant with DAPI |
Invitrogen |
Cat# P-36931 |
Hank’s Balanced Salt Solution (HBSS) |
Gibco |
Cat# 14175095 |
SUPERaseIn RNase Inhibitor |
Invitrogen |
Cat# AM2694 |
TRIzol Reagent |
Life Technologies |
Cat# 15596026 |
Denaturing Hypotonic Lysis buffer (DHL) |
Singh et al. (2014)
|
N/A |
Alt-R S.p. HiFi Cas9 Nuclease v3 |
Integrated DNA Technologies |
Cat# 1081060 |
Blasticidin S Hydrochloride Powder |
Research Products International |
Cat# B12200
|
Ultrapure DNase/RNase-Free Distilled Water |
Invitrogen |
Cat# 10977015 |
Sail Restriction Enzyme |
New England Biolabs |
Cat# R0138L |
Notl Restriction Enzyme |
New England Biolabs |
Cat# R3198L |
Proteinase K |
Thermo Scientific |
Cat# FEREO0491 |
Laemmli SDS-Sample Buffer |
Boston BioProducts |
Cat# BP-111 R |
‘Soft Elution Buffer’ |
Antrobus and Borner (2011)
|
N/A |
Dulbecco’s Phosphate Buffered Saline |
Corning |
Cat# 20-031-CV |
Tween 20 |
Fisher BioReagents |
Cat# BP337-500 |
Dithiothrieitol Solution |
Sigma-Aldrich |
Cat# 43816 |
Trypsin-EDTA |
Gibco |
Cat# 15400054 |
Odyssey Blocking Buffer |
Licor |
Cat# 927-40010 |
Dulbecco’s Modified Eagle Medium |
Sigma-Aldrich |
Cat# D7777 |
Heat-Inactivated Fetal Bovine Serum |
Corning |
Cat# MT35011CV |
All trans Retinoic Acid |
Sigma-Aldrich |
Cat# R2625 |
Lipofectamine 3000 |
Invitrogen |
Cat# L3000015 |
Poly-DL-Lysine |
Sigma-Aldrich |
Cat# P9011 |
Formaldehyde |
Fisher |
Cat# BP531-500 |
BSA (lyophilized powder) |
Sigma-Aldrich |
Cat# A9418 |
Triton X-100 |
Sigma-Aldrich |
Cat# X-100 |
Mowiol 4-88 Reagent |
Calbiochem |
Cat# 47-590-4100GM |
Sepharose GFP-Binder Beads |
Gift from Vladimir Gelfand Lab |
N/A |
Accutase Cell Detachment Solution |
Corning |
Cat# MT25058CI |
Matrigel hESC-Qualified Matrix |
Corning |
Cat# 08-774-552 |
ROCK Inhibitor |
Selleck Chemicals |
Cat# S1049 |
Lipofectamine Stem Transfection Reagent |
Invitrogen |
Cat# STEM00001 |
Chelex 100 Sodium form |
Sigma-Aldrich |
Cat# C7901 |
Stemflex Medium |
Gibco |
Cat# A3349401 |
B27 Plus Neuronal Culture System |
Gibco |
Cat# A3653401 |
Poly D-L-Ornithine |
Sigma |
Cat# P3655 (3000-7000 kDa) |
Laminin |
Invitrogen |
Cat# 23017-015 |
Neurobasal medium |
Invitrogen |
Cat# 21103-049 |
Glutamax 200mM |
Invitrogen |
Cat# 35050-061 |
B27 |
Invitrogen |
Cat# 17504-044 |
hsBDNF |
PeproTech |
Cat# 450-02 |
rnCNTF |
PeproTech |
Cat# 450-50 |
mmGDNF |
PeproTech |
Cat# 450-44 |
Horse Serum |
Sigma |
Cat# H1138-100ML |
BSA |
Gold Biotechnology |
Cat# A-421-50 |
4-20% Mini-PROTEAN® TGX™ Gel, 15 well, 15 μL |
Bio-Rad |
Cat# 456-1096 |
Nitrocellulose membrane/filter paper pack, pkg of 50 |
Bo-Rad |
Cat# 1620213 |
Protease inhibitor tables |
Roche |
Cat# 11873580001 |
NeuroMag paramagnetic beads |
Oz Biosciences |
Cat# NM50200 |
Magnetic plate |
Oz Biosciences |
Cat# MF10000 |
|
Critical commercial assays |
|
Pierce BCA Protein Assay Kit |
ThermoFisher Scientific |
Cat# 23227 |
AmpliTaq Gold 360 Master Mix |
Applied Biosystems |
Cat# 4398876 |
High Capacity cDNA Reverse Transcription Kit |
Applied Biosystems |
Cat# 436814 |
TaqMan Fast Advanced Master Mix |
Applied Biosystems |
Cat# 4444556 |
Taqman Gene Expression Assay, SLITRK2 |
ThermoFisher Scientific |
Hs01028461_s1 |
Taqman Gene Expression Assay, TCEAL2 |
ThermoFisher Scientific |
Hs04194669_sH |
Taqman Gene Expression Assay, PCDHA13 |
ThermoFisher Scientific |
Hs00259032_s1 |
Taqman Gene Expression Assay, HNRNPM |
ThermoFisher Scientific |
Hs01115690_m1 |
Taqman Gene Expression Assay, DNAJA4 |
ThermoFisher Scientific |
Hs00388055_m1 |
Taqman Gene Expression Assay, ELAVL4 |
ThermoFisher Scientific |
Hs00956610_mH |
Taqman Gene Expression Assay, GAPDH |
ThermoFisher Scientific |
Hs02786624_g1 |
NEBuilder HiFi DNA Assembly Cloning Kit |
New England Biolabs |
Cat# E5520S |
HiSpeed Plasmid Midi Kit |
Qiagen |
Cat# 12662 |
PureLink HiPure Plasmid Midiprep Kit |
Invitrogen |
Cat# K210005 |
|
Deposited data |
|
Sequence data, analyses, and resources related to the RIPseq of V5-KIF5AΔ and V5-KIF5AΔExon27 immunoprecipitation eluates |
This paper |
Gene Expression Omnibus GSE196539
|
Sequence data, analyses, and resources related to the RNA sequencing of KIF5AR1007K and isogenic control iMNs |
This paper |
Gene Expression Omnibus GSE196539
|
Sequence data, analyses and resources related to the mass spectrometry analysis of V5-KIF5AwT and V5-KIF5AΔExon27 immunoprecipitation eluates |
This paper |
ProteomeXchange; PXD031012 |
|
Experimental models: Cell lines |
|
COS-7 |
ATCC |
CRL-1651; RRID:CVCL_0224 |
SKNAS |
ATCC |
CRL-2137; RRID:CVCL_1700 |
HEK293FT |
Invitrogen |
R70007 |
Neuro2A |
ATCC |
CCL-131; RRID:CVCL_0470 |
|
Experimental models: Organisms/strains |
|
C57BL/6 female mice (primary neuron preps) |
Charles River Laboratories |
Cat# 027 |
|
Oligonucleotides |
|
sgRNA targeting CYBL locus - ATGTTGGAAGGATGAGGAAA |
Fernandopulle et al. (2018)
|
N/A |
Primer for HA-KIF5A Forward − ACTGACGCTAGCCACCATGTACCCATACGATGTTCCAGATTACGCTGGTGGTTCTGGTGGTGGTTCTGGTATGGCGGAGACCAACAACG |
This Paper |
N/A |
Primer for HA-KIF5A WT Reverse − AGAATCGGATCCTGTGGGAGATTAGCTGGCTG |
This Paper |
N/A |
Primer for HA-KIF5A Del27 Reverse − AGATACGGATCCCGAAGTTATGGTACCTTAGAAACTGA |
This Paper |
N/A |
Primer for HA-KIF5A C-Term Reverse − AGAATCGGATCCTTATCCATTGTCCATGTTGGCCTT |
This Paper |
N/A |
Primer for eGFP Forward − AGTCAGGCTAGCCACCATGGTGAGCAAGGGAGAGGAG |
This Paper |
N/A |
Primer for eGFP Reverse − AGATACGGATCCCTTGTACAGCTCGTCCATGCC |
This Paper |
N/A |
Primer for GFP-KIF5A Forward − |
This Paper |
N/A |
AGTCAGGGATCCGGTGGTTCTGGTGGTGGTTCTGGTATGGCGGAGACCAACAACG |
|
|
Primer for GFP-KIF5A WT Reverse − AGATACTCTAGATGTGGGAGATTAGCTGGCTG |
This Paper |
N/A |
|
Recombinant DNA |
|
DsRed-Mito |
Takara Bio |
Cat# 632421 |
pRK5:Myc-KIF5A |
Addgene |
Clone# 127616 |
pRK5-Myc-KIF5AWT-Halo |
This paper |
N/A |
pRK5-Myc- KIF5AΔExon27-Halo |
This paper |
N/A |
pRK5-Myc-KIF5AΔC-term-Halo |
This paper |
N/A |
pRK5-Myc-KIF5A1-560-Halo |
This paper |
N/A |
pcDNA4TO-K560-E236A-24xGCN4_v1-IRES-Puro |
Tanenbaum et al. (2014)
|
Addgene Clone #60909 |
pGW1-Kif5AWT |
This paper |
N/A |
pGW1-Kif5AΔExon27 |
This paper |
N/A |
pGW1-Kif5AΔC-term |
This paper |
N/A |
pGW1-tdTomato |
This paper |
N/A |
V5-Kif5AΔExon27 |
This paper |
Addgene Clone #15239 |
V5-Kif5AWT |
This paper |
Addgene Clone #15239 |
GFP-Kif5AWT |
This paper |
Addgene Clone #15239 |
HA-Kif5AWT |
This paper |
Addgene Clone #15239 |
Kif5AAExon27 |
This paper |
N/A |
pCMV-beta-Rat Lic1.FL-HA |
Tynan et al. (2000)
|
N/A |
pMyc-MOV10 |
Addgene |
Cat# 10977 |
RNT1-GFP |
Addgene |
Cat# 17708 |
HA-p62 |
Addgene |
Cat# 28027 |
pCDNA 3.1 (+) HA- KIF5A WT |
This Paper |
N/A |
pCDNA 3.1 (+) HA- KIF5A Del27 |
This Paper |
N/A |
pCDNA 3.1 (+) HA- KIF5A C-Term |
This Paper |
N/A |
pCDNA 3.1 (+) GFP-KIF5A WT |
This Paper |
N/A |
pCDNA 3.1 (+) GFP- KIF5A Del27 |
This Paper |
N/A |
|
Software and algorithms |
|
FastQC |
Babraham Institute |
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
MultiQC |
Ewels et al. (2016)
|
https://github.com/ewels/MultiQC
|
STAR aligner (2.7.0a) |
Dobin et al. (2013)
|
https://github.com/alexdobin/STAR
|
HTSeq |
Anders et al. (2015)
|
https://htseq.readthedocs.io/en/master/overview.html
|
DESeq2 |
Love et al. (2014)
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
rMATS version 4.0.2 |
Shenetal. (2014)
|
http://rnaseq-mats.sourceforge.net/
|
Metascape |
Zhou etal. (2019)
|
https://metascape.org/gp/index.html#/main/step1
|
rMAPS2 |
Hwang et al. (2020)
|
http://rmaps.cecsresearch.org/
|
ImageJ |
NIH |
https://imagej.nih.gov/ij/
|
MTrackJ |
NIH |
https://imagescience.org/meijering/software/mtrackj/
|
Volocity |
PerkinElmer |
https://www.perkinelmer.com
|
Prism 9 |
GraphPad |
https://www.graphpad.com/scientific-software/prism
|
Survival Analysis YOLO |
This paper |
https://drive.google.com/drive/folders/1V36q_9QjX_0SHbLS_IN2PPngOSLKYS1_?usp=sharing
|
Biorender |
Biorender |
https://www.biorender.com
|
AutoQuant x3 |
Media Cybernetics |
https://www.mediacy.com/79-products/autoquant-x3
|
Proteome Discoverer 2.1.1.21 |
Thermo Scientific |
https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html
|
Mascot Server 2.6.2 |
Matrix Science Ltd. |
http://www.matrixscience.com/
|
Scaffold 4.10.0 |
Proteome Software, Inc. |
https://www.proteomesoftware.com/products/scaffold-5
|
Peptide Prophet |
Keller et al. (2002); Nesvizhskii et al. (2003)
|
http://peptideprophet.sourceforge.net/
|
PyMOL |
The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC |
https://pymol.org/2/
|
I-TASSER |
Yang et al. (2015)
|
https://zhanggroup.org/I-TASSER/
|
|
Other |
|
Cytation 5 Cell Imaging Multi Mode Reader |
Agilent (BioTek) |
https://www.biotek.com/products/imaging-microscopy-cell-imaging-multi-mode-readers/cytation-5-cell-imaging-multi-mode-reader/
|
BioSpa 8 Automated Incubator |
Agilent (BioTek) |
https://www.biotek.com/products/software-robotics-robotics/biospa-8-automated-incubator/
|
Nikon Ti Eclipse |
Nikon |
Ti Eclipse |
Leica DMI6000 Widefield Microscope |
Leica Microsystems |
DMI6000 |
Anti-V5 Tagged Magnetic Beads |
MBL International |
Cat#M167-11 |
CFX 384 Real-Time PCR Detection System |
BioRad |
https://www.bio-rad.com/en-us/product/cfx384-touch-real-time-pcr-detection-system?ID=LJB22YE8Z
|
C1000 Touch Thermal Cycler |
BioRad |
https://www.bio-rad.com/en-us/sku/1851138-c1000-touch-thermal-cycler-with-384-well-reaction-module?ID=1851138
|
Trans-Blot Turbo Transfer System |
BioRad |
Cat# 1704150 |