|
|
Antibodies
|
|
| Anti-GFP antibody - ChIP Grade (1:300 for WB) |
Abcam |
Cat# ab290, RRID:AB_303395 |
| CD4 [EPR6855] antibody (1:500 for WB) |
Abcam |
Cat# ab133616, RRID:AB_2750883 |
| Cre recombinase antibody [7.23] (1:200 for WB) |
Abcam |
Cat# ab24607, RRID:AB_448179 |
| anti-SMAD5 antibody[3H9] (1:200 for WB) |
Novus Biologicals |
Cat# NBP2–37648 |
| FGFR1 Antibody (1:200 for WB) |
Novus |
Cat# NB100–2079, RRID:AB_10144921 |
| FGFR1 (phospho Y654) antibody (1:200 for WB) |
Abcam |
Cat# ab59194, RRID:AB_941585 |
| Monoclonal ANTI-FLAG® M2 antibody (1:400 for WB; 1:150 for IF) |
Sigma-Aldrich |
Cat# F1804, RRID:AB_262044 |
| HA tag antibody - ChIP Grade (1:400 for WB; 1:150 for IF) |
Abcam |
Cat# ab9110, RRID:AB_307019 |
| beta Tubulin antibody - Loading Control (1:500 for WB) |
Abcam |
Cat# ab6046, RRID:AB_2210370 |
| Anti-GAPDH antibody [EPR16891] (1:500 for WB) |
Abcam |
Cat# ab181602, RRID:AB_2630358 |
| IRDye 680RD Goat anti-Mouse IgG antibody (1:5,000 for WB) |
LI-COR Biosciences |
Cat# 926–68070, RRID:AB_10956588 |
| IRDye® 800CW Goat anti-Rabbit IgG (H + L) (1:5000 for WB) |
LI-COR Biosciences |
Cat# 926–32611 |
| Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (1:1,500 for IF) |
Thermo Fisher Scientific |
Cat# A-11029, RRID:AB_2534088 |
| Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 (1:150 for IF) |
Thermo Fisher Scientific |
Cat# A-11012, RRID:AB_2534079 |
| Customize rabbit anti-circFGFR1p |
Thermo Fisher Scientific |
Project# VJ2580 |
|
|
Bacterial and Virus Strains
|
|
| NEB® 10-beta Competent E. coli
|
New England Biolabs |
C3019H |
|
|
Chemicals, Peptides, and Recombinant Proteins
|
|
| SYBR™ Gold Nucleic Acid Gel Stain |
Thermo Fisher Scientific |
Cat# S11494 |
| BrightStar™-Plus Positively Charged Nylon Membrane |
Thermo Fisher Scientific |
Cat# AM10100 |
| Millennium™ RNA Markers |
Thermo Fisher Scientific |
Cat# AM7150 |
| Cycloheximide,≥93.0% (HPLC) |
Sigma-Aldrich |
Cat# 01810 |
| Puromycin Dihydrochloride |
Thermo Fisher Scientific |
Cat# A11138–03 |
| Pierce™ IP Lysis Buffer |
Thermo Fisher Scientific |
Cat# 87788 |
| Pierce™ Protein A/G Magnetic Beads |
Thermo Fisher Scientific |
Cat# 88803 |
| NuPAGE™ 4 to 12%, Bis-Tris, 1.5 mm, Mini Protein Gel, 10-well |
Thermo Fisher Scientific |
Cat# NP0335BOX |
| Corning® BioCoat™ Poly-D-Lysine 12 mm #1 German Glass Coverslip |
Corning |
Cat# 354086 |
| ON-TARGET plus non-targeting pool |
Dharmacon |
Cat# D-001810–10-05 |
| SMARTpool: ON-TARGETplus FGFR1 siRNA |
Dharmacon |
Cat# L-003131–00-0005 |
| Gibco FGF1 Recombinant Human Protein |
Thermo Fisher Scientific |
Cat# 13–241-013 |
| PrestoBlue™ Cell Viability Reagent |
Thermo Fisher Scientific |
Cat# A13261 |
| E-Gel™ EX Agarose Gels, 2% |
Thermo Fisher Scientific |
Cat# G402022 |
| NEB® 10-beta/Stable Outgrowth Medium |
New England Biolabs |
Cat# B9035S |
| Opti-MEM™ I Reduced Serum Medium |
Thermo Fisher Scientific |
Cat# 31985070 |
| Q5® Hot Start High-Fidelity 2X Master Mix |
New England Biolabs |
Cat# M0409L |
| TrypLE™ Express Enzyme (1X), no phenol red |
Thermo Fisher Scientific |
Cat# 12604013 |
| NEBNext® Ultra™ II Q5® Master Mix |
New England Biolabs |
Cat# M0544L |
| Invitrogen Ambion SUPERase·In RNase Inhibitor (20U/μL) |
Thermo Fisher Scientific |
Cat# AM2694 |
| SuperBlock Blocking Buffers |
Thermo Fisher Scientific |
Cat# 37517 |
| TURBO DNase (2U/μL) |
Thermo Fisher Scientific |
Cat# AM2238 |
| SuperScript IV Reverse Transcriptase |
Thermo Fisher Scientific |
Cat# 18090050 |
| Normal Rabbit IgG |
Sigma-Aldrich |
Cat# 12–370 |
| RIPA Lysis and Extraction Buffer |
Thermo Fisher Scientific |
Cat# 89900 |
| Halt Protease and Phosphatase Inhibitor Cocktails |
Thermo Fisher Scientific |
Cat# 78441 |
| RNaseR |
MCLAB Products |
Cat# RNASR-200 |
|
|
Critical Commercial Assays
|
|
| Lipofectamine™ 3000 Transfection Reagent |
Thermo Fisher Scientific |
Cat# L3000015 |
| Quick-DNA Microprep Plus Kit |
Zymo Research |
Cat# D4074 |
| NorthernMax™-Gly Kit |
Thermo Fisher Scientific |
Cat# AM1946 |
| RNeasy Mini Kit |
Qiagen |
Cat# 74004 |
| SuperScript™ IV One-Step RT-PCR System |
Thermo Fisher Scientific |
Cat# 12594100 |
| HiScribe™ T7 High Yield RNA Synthesis Kit |
New England Biolabs |
Cat# E2040S |
| GeneMorph II Random Mutagenesis Kit |
Agilent |
Cat# 200550 |
| DNA Clean & Concentrator-25 |
Zymo Research |
Cat# D4033 |
| Zymoclean Gel DNA Recovery Kit (uncapped columns) |
Zymo Research |
Cat# D4002 |
| Direct-zol RNA Microprep |
Zymo Research |
Cat# R2061 |
| RNA Clean & Concentrator-25 |
Zymo Research |
Cat# R1017 |
| RNA Clean & Concentrator-5 |
Zymo Research |
Cat# R1013 |
| Zymoclean Gel RNA Recovery Kit |
Zymo Research |
Cat# R1011 |
| NEBuilder® HiFi DNA Assembly Master Mix |
New England Biolabs |
Cat# E2621L |
| ZymoPURE II Plasmid Maxiprep Kit |
Zymo Research |
Cat# D4203 |
| Complete kit (optimized for Roche® LightCycler 480) |
Kapa Biosystems |
Cat# KK4854 |
| NEBuilder® HiFi DNA Assembly Master Mix |
New England Biolabs |
Cat# E2621L |
|
|
Deposited Data
|
|
| IRES screening, polysome profiling, and M2-seq sequencing |
This paper |
GEO: GSE178718
|
| Ribosome footprinting |
Chen et al., 2020
|
GEO: GSM3791725, GSM3791726, GSM3791727, GSM3791728, GSM3791729, and GSM3791730
|
| iPSC peptidomics |
Chen et al., 2020
|
PRIDE: PXD014031 |
| SCBC peptidomics |
Orre et al., 2019
|
ProteomeXchange: PXD006895 |
| GTEx peptidomics |
Jiang et al., 2020
|
ProteomeXchange: PXD016999 |
| K562/U2OS/H358 peptidomics |
This paper |
ProteomeXchange: PXD025233 |
| HLA class I peptidomes |
Bassani-Sternberg et al., 2015
|
PRIDE: PXD014031 |
| circFGFR1p IP-MS |
This paper |
ProteomeXchange: PXD024993 |
| K562/U2OS PRM-MS |
This paper |
ProteomeXchange: PXD025235 |
| circFGFR1p PRM-MS |
This paper |
ProteomeXchange: PXD025203 |
| QTI-seq |
Gao et al., 2015
|
SRA: 160745 |
|
|
Experimental Models: Cell Lines
|
|
| HEK293T |
ATCC |
Cat# CRL-3216; RRID: CVCL_0063 |
| HeLa |
ATCC |
Cat# CCL-2; RRID: CVCL_0030 |
| BJ |
ATCC |
Cat# CRL-2522; RRID:CVCL_3653 |
| U2OS |
ATCC |
Cat# HTB-96, RRID:CVCL_0042 |
|
|
Oligonucleotides
|
|
| qRT-PCR primers |
This paper |
Table S7
|
| IRES screening oligo library |
Weingarten-Gabbay et al., 2016
|
N/A |
|
|
Recombinant DNA
|
|
| Plasmid: pcDNA3.1(+) ZKSCAN1 Sense |
Addgene |
Cat# 60631 |
| Plasmid: pHAGE-FGFR1 |
Addgene |
Cat# 116740 |
| Plasmid: pUC19 Vector |
New England Biolabs |
Cat# N3041L |
| Plasmid: pLV-mCherry |
Addgene |
Cat# 36084 |
| Plasmid: mRuby-ZKSCAN-split-eGFP reporter |
This paper |
N/A |
| Plasmid: mRuby-IRES-eGFP reporter |
This paper |
N/A |
| Plasmid: autocatalytic-splicing circEGFP |
This paper |
N/A |
|
|
Software and Algorithms
|
|
| ZEN (blue edition) |
Carl Zeiss Microscopy |
https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html
|
| FlowJo_V10 |
FlowJo, LLC |
https://flowjo.com/solutions/flowjo/downloads
|
| Bowtie2 |
Langmead and Salzberg, 2012
|
https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.4/
|
| TopHat2 |
Kim et al., 2013
|
https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz
|
| M2-seq and M2-net |
Cheng et al., 2017
|
https://ribokit.github.io/M2seq/
|
| ViennaRNA |
Lorenz et al., 2011
|
https://www.tbi.univie.ac.at/RNA/
|
| MaxQuant |
Cox and Mann, 2008
|
https://www.maxquant.org/download_asset/maxquant/latest
|
| Trans Proteomic Pipeline |
Collaborative open-source |
http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
|
| Byonic |
Protein Metrics |
https://proteinmetrics.com/byos/
|
| Skyline 19.1.0.193 |
MacLean et al., 2010
|
https://skyline.ms/wiki/home/software/Skyline/page.view?name=install-administator-64
|
