| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-FLAG (M2), 1:500 | Sigma-Aldrich | Cat#F1804; RRID: AB_262044 |
| Rabbit monoclonal anti-ATPIF1 (D6P1Q), 1:1000 | Cell Signaling Technology | Cat#13268; RRID: AB_10949890 |
| Rabbit polyclonal anti-Clathrin Heavy Chain (P1663), 1:100 | Cell Signaling Technology | Cat#2410; RRID: AB_2083156 |
| Alexa Fluor 488 anti-rabbit, 1:500 | Invitrogen | Cat#A11070; RRID: AB_142134 |
| Alexa Fluor 594 anti-mouse, 1:500 | Invitrogen | Cat#A11005; RRID: AB_141372 |
| Rabbit monoclonal anti-V5-Tag (D3H8Q), 1:500 | Cell Signaling Technology | Cat#13202; RRID: AB_2687461 |
| Chicken polyclonal anti-BirA, 1:500 | BioFront Technologies | Cat#BID-CP-100, RRID: not available |
| Alexa Fluor 488 anti-mouse, 1:500 | Invitrogen | Cat#A11001, RRID: AB_2534069 |
| Alexa Fluor 488 anti-chicken, 1:500 | Invitrogen | Cat#A11039, RRID: AB_142924 |
| Alexa Fluor 594 anti-rabbit, 1:500 | Invitrogen | Cat#A-11037, RRID: AB_2534095 |
| Mouse monoclonal anti-EEA1, 1:100 | BD Transduction Laboratories | Cat#610457, RRID: AB_397830 |
| Alexa Fluor 555 anti-mouse, 1:500 | Invitrogen | Cat#A31570, RRID: AB_2536180 |
| Biological samples | ||
| human heart tissue of five adult cardiomyopathy patients: Sample 1: female, DCM, age range 55-60 Sample 2: male, DCM, age range 30-35 Sample 3: male, HCM, age range 40-45 Sample 4: male, HCM, age range 55-60 Sample 5: female, HCM, age range 50-55 |
Harvard Medical School, Boston USA, previously used in van Heesch et al.22 | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Alexa 647-conjugated transferrin | Invitrogen | Cat#T23366 |
| Lysyl Endopeptidase | Wako | Cat#125-05061 |
| Trypsin Gold | Promega | Cat#V5280 |
| PRISMA synthetic peptides on a cellulose membrane | JPT | PRISMA - peptides |
| Crude synthetic peptides for PRM assay | JPT | SpikeTides/Maxi SpikeTides |
| Proteinase K | Sigma-Aldrich | Cat#3115879001 |
| Poly-D-Lysine | Sigma-Aldrich | Cat#P0899-50MG |
| cOmplete, EDTA-free Protease Inhibitor Cocktail | Roche | Cat#11873580001 |
| synthetic peptides with TAT-sequence | Pepscan | custom |
| DAPI | Thermo Fisher | Cat#R37606 |
| Critical commercial assays | ||
| Duolink® In Situ Proximity Ligation Assay Starter Kit, Red, Mouse/Rabbit | Sigma-Aldrich | Cat#DUO92101-1KT |
| Alexa Fluor 594 Protein Labeling Kit | Thermo Fisher | Cat#A10239 |
| Dual Glo® Luciferase Assay System | Promega | Cat#E2920 |
| Deposited data | ||
| Cataloged set of 7,264 Ribo-seq ORFs | Mudge et al.2 | https://www.gencodegenes.org/pages/riboseq_orfs/ |
| MS data: PRISMA (microproteins >15aa) | This paper | ProteomeXchange (via PRIDE76): PXD033629, PXD033630 |
| MS data: microprotein pull-down with phosphosite identification | This paper | ProteomeXchange (via PRIDE76): PXD033631 |
| MS data: PRISMA (peptides3-15aa) | This paper | ProteomeXchange (via PRIDE76): PXD033651 |
| MS data: PRM | This paper | ProteomeXchange (via PRIDE76): PXD036997 |
| RNA-seq data for LINC01128 knockout and wild type cell lines | This paper | European Nucleotide Archive (ENA): PRJEB57619 |
| Public human ribosome profiling data used for detection of sORFs3-15aa | van Heesch et al.22 and Wang et al.23 | left ventricular heart tissue: EGA accession code EGAS0000100326322; kidney: EGA accession code EGAS0000100326322; liver: EGA accession code EGAS0000100326322 and ArrayExpress accession code E-MTAB-724723; brain: ArrayExpress accession code E-MTAB-724723; testis: ArrayExpress accession code E-MTAB-724723 |
| Ribosome profiling data of mouse and rat tissues | van Heesch et al.,22 Wang et al.,23 and Witte et al.50 | mouse heart: ENA accession code PRJEB2920822; mouse liver: ArrayExpress accession code E-MTAB-724723; mouse brain: ArrayExpress accession code E-MTAB-724723; mouse testis: ArrayExpress accession code E-MTAB-724723; rat heart: ENA accession code PRJEB3809650 and rat liver: ENA accession code PRJEB3809650 |
| RNA sequencing datasets of HEK293T cells | Schueler et al.77 | NCBI Sequence Read Archive (SRA) SRR1107836 and SRR1107837 |
| Microscopy data: original images from immunofluorescence stainings | This paper | Mendeley Data https://doi.org/10.17632/ckgdgty885.178 |
| Supplemental excel tables Tables S1, S2, S3, S4, and S5 | This paper | Mendeley Data https://doi.org/10.17632/ckgdgty885.178 |
| Experimental models: Cell lines | ||
| Brown Norway rat yolk sac carcinoma (BN16) cells | ATCC | ATCC® CRL-2180 |
| HeLa cells | kindly provided by A. Woehler, MDC | N/A |
| HeLa LINC01128-MP KO cells and wild type cells | Synthego Inc. | N/A |
| HEK293T/17 cells | ATCC | ATCC® CRL-11268 |
| K562 cells | kindly provided by T. Blankenstein, MDC | N/A |
| Software and algorithms | ||
| BLASTp (v.2.7.1) | Altschul79 | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| PhyloCSF | Lin et al.80 | https://github.com/mlin/PhyloCSF/wiki |
| PRANK (v.170427) | Löytynoja81 | http://wasabiapp.org/software/prank/ |
| STAR (v.2.5.2b) | Dobin et al.82 | https://github.com/alexdobin/STAR |
| BEDTools (v.2.27.1) | Quinlan83 | https://bedtools.readthedocs.io/en/latest/ |
| UCSC Liftover | Lee et al.84 | https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Liftover |
| Stringtie (v.1.2.1) | Pertea et al.85 | https://ccb.jhu.edu/software/stringtie/ |
| RepeatMasker (v.4.1.0) | Smit and Hubley86 | https://www.repeatmasker.org/RepeatMasker/ |
| MaxQuant (v.1.5.2.8. and v.1.6.0.1) | Cox and Mann56 | https://www.maxquant.org/ |
| R (v.3.6.1) | R Core Team87 | https://www.r-project.org/ |
| IUPred (v.1.0) | Dosztányi et al.36 | https://iupred2a.elte.hu/ |
| ‘elm_classes.tsv’ file (version 1.4; 15 January 2018) | Gouw et al.37 | http://elm.eu.org/ |
| gProfiler2 (v0.2.0) | Reimand et al.88 | https://cran.r-project.org/web/packages/gprofiler2/index.html |
| DESeq2 (v1.26.0) | Love et al.89 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| RiboseQC | Calviello et al.90 | https://github.com/ohlerlab/RiboseQC |
| PRICE (v1.0.3b) | Erhard et al.47 | https://github.com/erhard-lab/price |
| TIS Transformer | Clauwaert et al.48 | https://github.com/jdcla/TIS_transformer |
| MSFragger | Kong et al.91 | https://msfragger.nesvilab.org/ |
| Trans-Proteomic Pipeline | Deutsch et al.58 | http://www.tppms.org/ |
| Proteomapper (v.1.5) | Mendoza et al.92 | http://www.tppms.org/tools/pm/ |
| Skyline (v21.02) | MacLean et al.93 | https://skyline.ms/project/home/software/Skyline/begin.view |
| Fiji | Schindelin et al.94 | https://imagej.net/software/fiji/ |
| NetMHCpan-4.1 | Reynisson et al.95 | https://services.healthtech.dtu.dk/service.php?NetMHCpan-4.1 |
| ORFquant (v1.00) | Calviello et al.46 | https://github.com/lcalviell/ORFquant |
| Other | ||
| Python, R and Bash scripts used for the analysis | This paper | Zenodo https://doi.org/10.5281/zenodo.755381796 Github: https://github.com/jorruior/riboseq_orfs_analyses |
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