Key resources
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-ATF4 (1:1000) | Cell Signaling Technology | Cat# 11815 RRID: AB_2616025 |
| Mouse monoclonal anti-β-Actin (1:5000) | Sigma-Aldrich | Cat# A5441 RRID: AB_476744 |
| Donkey anti-Rabbit IgG (1:10000) | LI-COR Biosciences | Cat# 925-68073 RRID: AB_2716687 |
| Goat anti-mouse IgG (1:10000) | LI-COR Biosciences | Cat# 925-32210 RRID: AB_2687825 |
| Bacterial and Virus Strains | ||
| Escherichia coli:OP50 | Caenorhabditis Genetics Center | RRID:WB-STRAIN:OP50 |
| Escherichia coli: HT115 (DE3) | Caenorhabditis Genetics Center | RRID:WB-STRAIN:HT115(DE3) |
| Ahringer C. elegans RNAi library | Source BioScience | http://www.sourcebioscience.com/products/life-science-research/clones/rnai-resources/c-elegans-rnai-collection-ahringer/ |
| Biological Samples | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| Cycloheximide | Sigma-Aldrich | Cat# C6255 |
| Doxycycline | Sigma-Aldrich | Cat# D9891 |
| Amoxicillin | Sigma-Aldrich | Cat# A8523 |
| DMSO | Sigma -Aldrich | Cat# D8418 |
| 5-FU | Sigma -Aldrich | Cat# f6627 |
| Sodium azide | Sigma-Aldrich | Cat# s8032 |
| FCCP | Abcam | Cat# ab120081 |
| Critical Commercial Assays | ||
| BCA protein assay Reagent A | Thermo Fisher Scientific | Cat# 23223 |
| TRIzol (LS) | Invitrogen | Cat# 15596026 (#10296010) |
| RNeasy MinElute Cleanup Kit | Qiagen | Cat# 74204 |
| NEBNext Ultra Directional RNA Library Prep Kit | NEB | Cat# E7420 |
| rRNA depletion kit | NEB | Cat# E6310 |
| QuantiTect Reverse Transcription Kit | Qiagen | Cat# 205314 |
| LightCycler® 480 SYBR Green I Master | Roche | Cat# 04887352001 |
| Deposited Data | ||
| C. elegans and Mouse RNA-seq data | This paper | GEO: GSE122097 |
| C. elegans Proteomics data | This paper | PRIDE: PXD009223 |
| BXD mouse liver proteome data (reprocessed) | This paper | Table S1 |
| BXD mouse liver proteome data | Genenetwork.org | GN540 |
| BXD mouse multi tissue proteome data | Molecular and Cellular Proteomics Journal | DOI: 10.1074/mcp.RA118.000554 |
| Experimental Models: Cell Lines | ||
| Human: K562 cells | ATCC | CCL-243 RRID:CVCL_0004 |
| Experimental Models: Organisms/Strains | ||
| C. elegans: N2 Bristol | Caenorhabditis Genetics Center (CGC); http://cbs.umn.edu/cgc/home | CGC:10570 RRID:WB-STRAIN: N2_(ancestral) |
| C. elegans: atfs-1(cmh15) | (Deng et al., 2019) | NA |
| Mouse: C57BL/6J germ-free | Micalis Institute (INRA Research Center of Jouy-en-Josas) | NA |
| Oligonucleotides | ||
| F35G12.2 forward primer: 5’- ACTGCGTTCATCCGTGCCGC-3’ | Sigma-Aldrich | NA |
| F35G12.2 reverse primer: 5’-TGCGGTCCTCGAGCTCCTTC-3’ | Sigma-Aldrich | NA |
| pmp-3 forward primer: 5’-GCTGGAGTCACTCATCGTGTTA -3’ | Sigma-Aldrich | NA |
| pmp-3 reverse primer: 5’- CCGGCCAATCATCCTCTTGA -3’ | Sigma-Aldrich | NA |
| mrps-5 forward primer: 5’-ACTGGCCGAACGAAAAGGTCT -3’ | Sigma-Aldrich | NA |
| mrps-5 reverse primer: 5’-AGTGGAAATCGGTGACGCCACAA -3’ | Sigma-Aldrich | NA |
| atf-5 forward primer: 5’- GTGCGAAGAAATCGAGCGTC -3’ | Sigma-Aldrich | NA |
| atf-5 reverse primer: 5’- GCTCCAACTCGGATACCTGAT -3’ | Sigma-Aldrich | NA |
| skn-1 forward primer: 5’- TCAATTTATGGAGTGTCGTCCA -3’ | Sigma-Aldrich | NA |
| skn-1 reverse primer: 5’- CCGTTGATCATCACGCCAAC -3’ | Sigma-Aldrich | NA |
| eif-3.c forward primer: 5’- TTTCCAGGAAGGAACGAGCG -3’ | Sigma-Aldrich | NA |
| eif-3.c reverse primer: 5’- CCGTCTTGTCCTTGTCCTCC -3’ | Sigma-Aldrich | NA |
| eif-3.g forward primer: 5’- GCATTAACGCAATGGCTCCC -3’ | Sigma-Aldrich | NA |
| eif-3.g reverse primer: 5’- TCGGTACGTGTTCCATCAGC -3’ | Sigma-Aldrich | NA |
| rpl-14 forward primer: 5’- CAAGCTCACCGACTTCGAGA -3’ | Sigma-Aldrich | NA |
| rpl-14 reverse primer: 5’- GAGCTCCACTCGGACGATTC -3’ | Sigma-Aldrich | NA |
| Recombinant DNA | ||
| Software and Algorithms | ||
| R (v3.4.3) | R | https://www.r-project.org |
| FastQC | (Andrews, 2010) | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| iGraph v1.2.1 package | iGraph | https://CRAN.R-project.org/package=igraph |
| RTA v2.7.7 | Illumina, Real-Time Analysis | Illumina.com |
| Bcl2fastq v2.17 | Illumina | Illumina.com |
| Trimmomatic v0.32 | (Bolger et al., 2014) | http://www.usadellab.org/ |
| HISAT2 v2.0.4 | (Kim et al., 2015) | https://ccb.jhu.edu/software/hisat2/index.shtml |
| HTSeq v0.6.1 | (Anders et al., 2015) | https://htseq.readthedocs.io/en/release_0.10.0/ |
| Comet v2016.01 r3 | doi: 10.1002/pmic.201200439 | v2016.01 r3 |
| OpenSWATH v2.1.0 | http://www.openswath.org/ | |
| MSstats v3.12.0 | http://msstats.org/ | |
| Limma/voom | (Ritchie et al., 2015)/(Law et al.,2014) | https://bioconductor.org/packages/release/bioc/html/limma.html |
| edgeR | (Robinson et al., 2010) | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| HiSeq control software HCS v3.4.0 | Illumina | https://support.illumina.com/downloads/hiseq-x-hcs-v3-4-0.html |
| Bioconductor v3.5 | Bioconductor | https://www.bioconductor.org/install/ |
| GraphPad Prism v7.03 | GraphPad Software, Inc. | https://www.graphpad.com/scientific-software/prism/ |
| ImageJ | National Institutes of Health | https://imagej.nih.gov/ij/ |
| Bruker TASQ software v2.1.22.3 | Bruker | https://www.bruker.com/products/mass-spectrometry-and-separations/ms-software/tasq/tasq-software.html |
| Other | ||