Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Biological sample (Xenopus laevis) |
Xenopus laevis | NASCO | Cat# LM00715 (male); RRID:XEP_Xla100; Cat# LM00535 (female); RRID:XEP_Xla |
|
| Cell line (Homo-sapiens) |
SH-SY5Y | ATCC | Cat# CRL-2266; RRID:CVCL_0019 | |
| Antibody | anti-RPS3A (Rabbit polyclonal) | Abcam | Cat# ab194670; RRID:AB_2756396 |
ICC/PLA (1:100) WB (1:1000) |
| Antibody | Anti-Neuropilin-1 (Rabbit monoclonal) |
Abcam | Cat# ab81321; RRID:AB_1640739 |
ICC/PLA (1:100) WB (1:2000) IP (5 µg) |
| Antibody | Anti-Neuropilin-1 (Mouse monoclonal) |
Proteintech | Cat# 60067–1-Ig; RRID:AB_2150840 |
ICC (1:100) |
| Antibody | Anti-DCC (mouse monoclonal |
BD Biosciences | Cat# 554223; RRID:AB_395314 |
ICC/PLA (1:100) WB (1:1000) IP (5 µg) |
| Antibody | Anti-RPL5 (rabbit polyclonal | Proteintech | Cat# 15430–1-AP; RRID:AB_2238681 |
ICC/PLA (1:100) |
| Antibody | Anti-RPS4X (Rabbit polyclonal) |
Proteintech | Cat# 14799–1-AP; RRID:AB_2238567 |
PLA (1:100) WB (1:1000) |
| Antibody | Anti-RPL10A (Rabbit polyclonal) | Proteintech | Cat# 16681–1-AP; RRID:AB_2181281 |
PLA (1:100) WB (1:500) |
| Antibody | Anti-RPS23 (mouse monoclonal) | Abcam | Cat#: ab57644; RRID:AB_945314 |
PLA (1:100) WB (1:1000) |
| Antibody | Anti-RPS26 (Rabbit polyclonal |
Proteintech | Cat# 14909–1-AP; RRID:AB_2180361 |
WB (1:500) |
| Antibody | Anti-Robo2 (goat polyclonal) |
R and D Systems | Cat# AF3147; RRID:AB_2181857 |
WB (1:250) |
| Antibody | Anti-EphB2 (mouse monoclonal) |
Santa Cruz | Cat# sc130068; RRID:AB_2099958 |
WB (1:100) IP (5 µg) |
| Antibody | Anti-EphB2 (mouse monoclonal) |
Thermo Fisher Scientific | Cat# 37–1700; RRID:AB_2533302 |
PLA (1:100) |
| Antibody | Anti-Staufen1 (Rabbit polyclonal) |
Abcam | Cat# ab73478; RRID:AB_1641030 |
ICC (1:100) WB (1:500) |
| Antibody | Anti-hnRNPA2B1 (Rabbit polyclonal) |
Abcam | Cat# ab31645; RRID:AB_732978 |
ICC/PLA (1:100) |
| Antibody | Anti-RPS14 (Rabbit polyclonal) |
Abcam | Cat# ab174661 | ICC (1:100) |
| Antibody | Anti-ß-Catenin (Rabbit polyclonal) |
Sigma-Aldrich | Cat# C2206; RRID:AB_476831 |
ICC (1:500) |
| Antibody | Anti-hnRNPH1 | Abcam | Cat# ab154894 | ICC (1:500) |
| Antibody | Anti-IgG (Rabbit) | Abcam | Cat# ab37415; RRID:AB_2631996 |
PLA (1:100) IP (5 µg) |
| Antibody | Anti-IgG1 (Mouse) | R and D Systems | Cat# MAB002; RRID:AB_357344 | PLA (1:100) IP (5 µg) |
| Antibody | Anti-IgG2b (Mouse) | R and D Systems | Cat# MAB004; RRID:AB_357346 | IP (5 µg) |
| Antibody | Anti-IgG (Goat) | R and D Systems | Cat# AB-108-C; RRID:AB_354267 |
IP (5 µg) |
| Antibody | Anti-Puromycin-Alexa Fluor 488 conjugate (mouse monoclonal) |
Millipore | Cat# MABE343-AF488; RRID:AB_2736875 | ICC (1:200) |
| Antibody | Anti-RPL19 (mouse monoclonal) |
Abcam | Cat#ab58328; RRID:AB_945305 |
WB (1:1000) |
| Antibody | Anti-FxR | Gift from Dr. Edward Khandjan, University of Quebec | N/A | WB (1:1000) |
| Antibody | Anti-pERK1/2 | Cell Signaling | Cat# 9101; RRID:AB_331646 |
ICC (1:250) |
| Antibody | Goat-anti-rabbit Alexa Fluor 568 |
Abcam | Cat# ab150077; RRID:AB_2630356 |
ICC (1:1000) |
| Antibody | Goat-anti-mouse Alexa Fluor 568 |
Abcam | Cat# ab150117; RRID:AB_2688012 |
ICC (1:1000) |
| Antibody | Goat-anti-mouse-HRP | Abcam | Cat# ab6789; RRID:AB_955439 |
WB (1:15000) |
| Antibody | Goat-anti-rabbit-HRP | Abcam | Cat#: ab97080; RRID:AB_10679808 |
WB (1:15000) |
| Commercial assay or kit | RNeasy mini kit | Qiagen | Cat# 74104 | |
| Commercial assay or kit | SuperScript III First-strand Synthesis kit |
Thermo Fisher Scientific | Cat# 18080051 | |
| Commercial assay or kit | Quantitect SYBR green PCR kit | Qiagen | Cat# 204143 | |
| Commercial assay or kit |
KAPA HyperPrep kit | Roche | Cat# KK8503 | |
| Commercial assay or kit |
NextSeq 500/550 high output v2 kit (150 cycles) |
Illumina | Cat# FC-404–2002 | |
| Commercial assay or kit | Duolink In situ PLA Detection reagents green |
Sigma-Aldrich | Cat# DUO92014 | |
| Commercial assay or kit |
Duolink In situ PLA Detection reagents red |
Sigma-Aldrich | Cat# DUO92008 | |
| Commercial assay or kit |
Duolink In situ PLA probe Anti-Rabbit PLUS | Sigma-Aldrich | Cat# DUO92002 | |
| Commercial assay or kit |
Duolink In situ PLA probe Anti-Mouse MINUS |
Sigma-Aldrich | Cat# DUO92004 | |
| Chemical compound, drug, reagent |
Cycloheximide | Sigma Aldrich | Cat# C4859 | |
| Chemical compound, drug, reagent |
RNase A | Ambion | Cat# EN0531 | |
| Chemical compound, drug, reagent |
RNase T1 | Ambion | Cat# EN0541 | |
| Chemical compound, drug, reagent |
Puromycin | Sigma-Aldrich | Cat# P8833 | |
| Chemical compound, drug, reagent |
Recombinant mouse Netrin-1 | R and D systems | Cat# 1109-N1 | |
| Chemical compound, drug, reagent |
Recombinant human Sema3A | R and D systems | Cat# 1250-S3 | |
| Chemical compound, drug, reagent |
Dynasore | Sigma-Aldrich | Cat# D7693 | |
| Chemical compound, drug, reagent | SUPERase In RNAse inhibitor | Ambion | Cat# AM2696 | |
| Software, algorithm | Volocity | PerkinElmer | Version 6.0.1; RRID:SCR_002668 |
|
| Software, algorithm |
GraphPad Prism | GraphPad | v.5; RRID:SCR_002798 |
|
| Software, algorithm |
R | Other | v.3.2.2; RRID:SCR_001905 |
https://www.r-
project.org |
| Software, algorithm |
MATLAB | Mathworks | v.R2016b; RRID:SCR_001622 | |
| Software, algorithm | HISAT2 | Other | v.2.1.0; RRID:SCR_015530 | https://ccb.jhu.edu/software/hisat2/index.shtml |
| Software, algorithm | Cufflinks | Other | v.2.2.1; RRID:SCR014597 |
http://cole-trapnell-lab.github.io/cufflinks/ |