KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-FLAG | Sigma Aldrich | F3165 |
| Mouse anti-eIF2α | Santa Cruz | 2103S |
| Rabbit anti-eIF4G | Cell Signaling | 2498S |
| Rabbit anti-eIF4A | Cell Signaling | 2490S |
| Mouse anti-eIF4E | Santa Cruz Biotechnology | sc-9976 |
| Rabbit anti-4E-BP1 total | Cell Signaling | 9644T |
| Rabbit anti-4E-BP1 pS65 | Cell Signaling | 9451T |
| Mouse anti-puromycin | EMD Millipore | MABE 343 |
| Goat anti-mouse HRP conjugated secondary antibody | Jackson ImmunoResearch | 115-035-062 |
| Goat anti-Rabbit HRP conjugated secondary antibody | Jackson ImmunoResearch | 111-035-144 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Puromycin | Gibco | A11138–03 |
| Actinomycin D | Sigma | A1410 |
| Recombinant RtcB enzyme | Donovan et al., RNA 2017. | Purified in-house |
| Nuclease treated Rabbit Reticulocyte Lysate | Promega | L4960 |
| Critical Commercial Assays | ||
| EasyTag EXRESS35S Protein Labeling mix | Perkin Elmer | NEG772002MC |
| MEGAshortscript™ T7 Transcription Kit | Thermo Fisher | Cat No. AM1354 |
| RNeasy Mini Kit | Qiagen | Cat No. 74106 |
| High Capacity Reverse Transcriptase kit | Applied Biosystems | Cat No. 4368814 |
| CircLigase | Epicenter | Cat No. CL9021K |
| Power SYBR Green PCR Master Mix | Life Technologies | Cat No. 4367659 |
| BioAnalyzer RNA 6000 Nano Kit | Agilent | Cat No. 5067–1511 |
| HiSeq 2000 | Illumina | N/A |
| Deposited Data | ||
| Poly-A+ RNAseq of poly I:C treated A549 cells with spike-in control | This paper | GSE123034 |
| RTCB-seq of poly I:C treated A549 cells | This paper | GSE131130 |
| RNA-seq analysis of RNase L-driven mRNA decay in cell-free systems – used for REML (see software and algorithms) | Rath et al. PNAS 2015. | GSE75530 |
| Experimental Models: Cell Lines | ||
| A549 cells | Susan Weiss, University of Pennsylvania. | N/A |
| Oligonucleotides | ||
| Oligonucleotides used for RtcB RNA-seq | Donovan et al., RNA 2017. | See Table S4 |
| qPCR primers used for mRNA steady state and half-life quantitation | This paper | See Table S5 |
| Software and Algorithms | ||
| RtcB RNA-seq mapping software | This paper | Described in the methods |
| GelQuant.NET | Biochem Lab Solutions | http://biochemlabsolutions.com/ |
| Welch two-tailed unpaired t-test, James McCaffrey Implementation | Microsoft | https://msdn.microsoft.com/en-us/magazine/mt620016.aspx |
| TopHat 2 | Kim et al., Genome Biol. 2013. | Used via pipelines developed by Lewis-Sigler Institute for Integrative Genomics on Galaxy.princeton.edu. |
| HTSEQ-count | Anders et al., Bioinformatics. 2015. | Used via pipelines developed by Lewis-Sigler Institute for Integrative Genomics on Galaxy.princeton.edu. |
| Integrated Genome Browser (IGV) | Robinson et al., Nature Biotechnology 2011. | https://software.broadinstitute.org/software/igv/ |
| Proteome Discoverer 2.2 | Thermo Scientific, USA | Used by the Princeton University Proteomics & Mass Spectrometry Core |
| Scaffold version 4.8.4 | Proteome Software Inc., Portland, OR | Used by the Princeton University Proteomics & Mass Spectrometry Core |
| Protein Prophet algorithm | Nesvizhskii et al., Anal Chem. 2003. | Used by the Princeton University Proteomics & Mass Spectrometry Core |