| Strain, strain background (Saccharomyces cerevisiae) |
MATa his3-∆1 leu2-∆0 met15∆0 ura3∆0 |
Research Genetics |
BY4741 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
MATa gcn4::kanMX4 his3∆1 leu2∆0 met15∆0 ura3∆0 |
Research Genetics |
249 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 tma64∆::kanMX4 |
Research Genetics |
4051 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 tma22∆::kanMX4 |
Research Genetics |
6812 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 tma20∆::kanMX4 |
Research Genetics |
328 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 tma64∆::hygMX4 tma20∆::kanMX4 |
Young et al., 2018 |
H4520 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
MATa his3∆1 leu2∆0 met15∆0 ura3∆0 tma64∆::hygMX4 tma20∆::kanMX5 |
Young et al., 2018 |
H4521 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
MATa ura3-52 trp1-∆63 leu2-3,−112 his4-303 |
Valásek et al., 2004 |
H2994 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
MATa ura3-52 leu2-3 leu2-112 trp1-∆63 his4-303(AUU) kanMX6::PGAL1-RPS26A rps26b∆::hphMX6 |
This study |
JVY09 |
|
| Recombinant DNA reagent |
FLUC reporter with 70nt synthetic 5'UTR with (CAA)n repeats in YCplac33 |
Sen et al., 2016 |
FJZ526 |
Plasmid |
| Recombinant DNA reagent |
FLUC reporter with cap-proximal SL with ∆G of −10.5 kcal/mol in synthetic 5’UTR in YCplac33 |
Sen et al., 2016 |
FJZ683 |
Plasmid |
| Recombinant DNA reagent |
FLUC reporter with cap-proximal SL with ∆G of −5.7 kcal/mol in synthetic 5’UTR in YCplac33 |
Sen et al., 2016 |
FJZ685 |
Plasmid |
| Recombinant DNA reagent |
FLUC reporter with cap-distal SL with ∆G of −10.5 kcal/mol in synthetic 5’UTR in YCplac33 |
Sen et al., 2016 |
FJZ688 |
Plasmid |
| Recombinant DNA reagent |
FLUC reporter with cap-distal SL with ∆G of −5.7 kcal/mol in synthetic 5’UTR in YCplac33 |
Sen et al., 2016 |
FJZ690 |
Plasmid |
| Recombinant DNA reagent |
GCN4-lacZ (uORFs1-4) in YCp50 |
Hinnebusch, 1985 |
p180 |
Plasmid |
| Chemical compound, drug |
Cycloheximide |
Sigma |
Cat# C7698 |
|
| Chemical compound, drug |
Complete EDTA-free Protease Inhibitor cocktail Tablet |
Roche |
Cat# 1873580001 |
|
| Chemical compound, drug |
Sulfometuron Methyl |
CHEM SERVICE |
Cat# PS-1074 |
|
| Other |
RNase I |
Ambion |
Cat# AM2294 |
enzyme |
| Other |
T4 RNA ligase 2 |
New England Biolabs |
Cat# M0242L |
enzyme |
| Other |
T4 Polynucleotide kinase |
New England Biolabs |
Cat# M0201L |
enzyme |
| Other |
Superscript III |
Invitrogen |
Cat# 18080044 |
enzyme |
| Other |
Circ Ligase ssDNA Ligase |
Epicentre |
Cat# CL4111K |
enzyme |
| Other |
T4 Rnl2(tr) K227Q |
New England Biolabs |
Cat# M0351S |
enzyme |
| Other |
RecJ exonuclease |
Epicentre |
Cat# RJ411250 |
enzyme |
| Other |
Yeast 5’-deadenylase |
New England Biolabs |
Cat# M0331S |
enzyme |
| Other |
Protoscript II |
New England Biolabs |
Cat# M0368L |
enzyme |
| Other |
CircLigase II |
Epicentre |
Cat# CL9025K |
enzyme |
| Other |
Phusion polymerase (F-530) |
New England Biolabs |
Cat# M0530S |
enzyme |
| Other |
GlycoBlue |
Invitrogen |
Cat# AM9516 |
Blue dye covalently linked to glycogen |
| Commercial assay, kit |
fragmentation reagent |
Ambion |
Cat# AM8740 |
|
| Commercial assay, kit |
miRNeasy Mini Kit |
Qiagen |
Cat# 217004 |
|
| Commercial assay, kit |
Ribo-Zero Gold rRNA Removal Kit |
Illumina |
Cat# MRZ11124C |
|
| Commercial assay, kit |
Bioanalyzer using the High Sensitivity DNA Kit |
Agilent |
Cat# 5067–4626 |
|
| Commercial assay, kit |
Oligo Clean and Concentrator column |
Zymo Research |
Cat# D4060 |
|
| Other |
Notched box-plots |
http://shiny.chemgrid.org/boxplotr/ |
|
Web-based tool |
| Other |
Gene ontology analysis |
https://biit.cs.ut.ee/gprofiler/gost |
|
Web-based tool |
| Other |
Spearman’s correlation calculator |
https://www.wessa.net/rwasp |
|
Web-based tool |
| Software, algorithm |
ggplot2, R package |
https://cran.r-project.org/web/packages/ggplot2/index.html |
|
|
| Software, algorithm |
GeneOverlap, R package |
https://www.bioconductor.org/packages/release/bioc/html/GeneOverlap.html |
|
|
| Software, algorithm |
Bowtie |
Langmead et al., 2009 |
|
|
| Software, algorithm |
TopHat |
Trapnell et al., 2009 |
|
|
| Software, algorithm |
Hisat2 |
https://github.com/DaehwanKimLab/hisat2 |
|
|
| Software, algorithm |
R script for DESeq2, R package |
https://github.com/hzhanghenry/RiboProR |
|
|
| Software, algorithm |
Integrative Genomics Viewer |
Robinson et al., 2011 |
|
|
| Software, algorithm |
Weblogo analysis |
Crooks et al., 2004 |
|
|
