| Antibodies |
| PA28α Antibody |
Cell Signaling Tech |
Cat#: 2408S; RRID:AB_2170937 |
| PA28β Antibody |
Cell Signaling Tech |
Cat#: 2409S; RRID:AB_2171085 |
| Monoclonal ANTI-FLAG® M2 antibody produced in mouse |
Sigma-Aldrich |
Cat#: F1804-200UG; RRID:AB_262044 |
| HA-Tag (C29F4) Rabbit mAb |
Cell Signaling Tech |
Cat#: 3724S; RRID:AB_1549585 |
| HA-Tag (6E2) Mouse mAb |
Cell Signaling Tech |
Cat#: 2367S; RRID:AB_10691311 |
| Vinculin (E1E9V) XP® Rabbit mAb |
Cell Signaling Tech |
Cat#: 13901S; RRID:AB_2728768 |
| GAPDH (14C10) Rabbit mAb |
Cell Signaling Tech |
Cat#: 2118S; RRID:AB_561053 |
| DDX42 polyclonal antibody rabbit |
Bethyl Laboratories |
Cat#: 303-353A; RRID:AB_10951853 |
| Anti-β-Actin Antibody (C4) |
Santa Cruz Biotechnology |
Cat#: sc-47778; RRID:AB_626632 |
| β-Actin (13E5) Rabbit mAb |
Cell Signaling Tech |
Cat#: 4970S; RRID:AB_2223172 |
| SF3B1 (D7L5T) Rabbit mAb |
Cell Signaling Tech |
Cat#: 14434S; RRID:AB_2798479 |
| p27 Kip1 (D69C12) XP® Rabbit mAb |
Cell Signaling Tech |
Cat#: 3686S; RRID:AB_2077850 |
| Anti-rabbit IgG, HRP-linked Antibody |
Cell Signaling Tech |
Cat#: 7074S; RRID:AB_2099233 |
| Anti-mouse IgG, HRP-linked Antibody |
Cell Signaling Tech |
Cat#: 7076S; RRID:AB_330924 |
| rabbit anti-goat IgG-HRP |
Santa Cruz Biotechnology |
Cat#: sc-2768; RRID:AB_656964 |
| InVivoMAb anti-human MHC Class I (HLA-A, HLA-B, HLA-C) Clone: W6/32 |
BioXCell |
Cat#: BE0079; RRID:AB_1107730 |
| IRDye® 680RD Goat anti-Rabbit IgG Secondary Antibody |
VWR |
Cat#: 926-68071; RRID:AB_10956166 |
| IRDye® 800CW Goat anti-Rabbit IgG Secondary Antibody |
VWR |
Cat#: 925-32211; RRID:AB_2651127 |
| IRDye® 680RD Goat anti-Mouse IgG Secondary Antibody |
VWR |
Cat#: 926-68070; RRID:AB_10956588 |
| IRDye® 800CW Goat anti-Mouse IgG Secondary Antibody |
VWR |
Cat#: 926-32210; RRID:AB_621842 |
| PE anti-mouse H-2Kb/H-2Db Antibody |
BioLegend |
Cat#: 114608; RRID:AB_313599 |
| PE Mouse IgG2a, κ Isotype Ctrl Antibody |
BioLegend |
Cat#: 400211; RRID:AB_326460 |
| APC anti-mouse H-2Kb bound to SIINFEKL Antibody |
BioLegend |
Cat#: 141606; RRID:AB_11219595 |
| APC Mouse IgG1, κ Isotype Ctrl Antibody |
BioLegend |
Cat#: 400120; RRID:AB_2888687 |
| APC/Cyanine7 Mouse IgG1, κ Isotype Ctrl Antibody |
BioLegend |
Cat#: 400128; RRID:AB_2892538 |
| Bacterial and virus strains |
| NEB 5-alpha Competent E. coli (High Efficiency) |
New England Biolabs |
Cat#: C2987H |
| Chemicals, peptides, and recombinant proteins |
| MEM Non-Essential Amino Acids Solution (100X) |
Thermo Scientific |
Cat#: 11140050 |
| Lipofectamine™ 2000 Transfection Reagent |
Thermo Scientific |
Cat#: 11668019 |
| Polybrene |
Santa Cruz Biotechnology |
Cat#: sc-134220A |
| Geneticin™ Selective Antibiotic (G418 Sulfate) |
Thermo Scientific |
Cat#: 10131035 |
| Pladienolide B |
Tocris Bioscience |
Cat#: 60-705-00U |
| Desthiobiotin polyethyleneoxide iodoacetamide |
Santa Cruz Biotechnology |
Cat#: sc-300424 |
| Tetramethylrhodamine (TAMRA) azide |
Synthesized in-house |
N/A |
| Biotin-PEG4-azide |
ChemPep |
Cat#: 271606 |
| SuperSignal West Pico PLUS Chemiluminescent Substrate |
Thermo Scientific |
Cat#: 34580 |
| Novex 4-20% Tris-Glycine Mini Gels |
Invitrogen |
Cat#: XP04205BOX |
| Nitrocellulose western blotting membrane, 0.45 μM |
GE Healthcare Amersham |
Cat#: 10600002 |
| Affi-Gel 10 Gel |
Bio-rad |
Cat#: 1536046 |
| DMSO |
Corning |
Cat#: 25-950-CQC |
| EDTA (0.5M, pH 8.0) |
Invitrogen |
Cat#: AM9260G |
| Urea |
Fisher Scientific |
Cat#: M1084871000 |
| Iodoacetamide |
Sigma-Aldrich |
Cat#: I1149-25G |
| Dithiothreitol (DTT) |
Fisher Bioreagents |
Cat#: BP172-25 |
| T ris(benzyltriazolylmethyl)amine (TBTA) |
TCI |
Cat#: T2993 |
| Copper(II) sulfate, anhydrous |
Sigma-Aldrich |
Cat#: 451657-10G |
| Tris(2-carboxyethyl)phosphine HCl (TCEP) |
Sigma-Aldrich |
Cat#: 75259 |
| Sequencing grade modified trypsin |
Promega |
Cat#: V5111 |
| Lysyl Endopeptidase, Mass Spectrometry Grade (Lys-C) |
Fujifilm Wako |
Cat#: 125-05061 |
| Streptavidin agarose resin |
Fisher Scientific |
Cat#: 20349 |
| Micro bio-spin column |
Bio-rad |
Cat#: 7326204 |
| Tween 20 |
Fisher Bioreagents |
Cat#: BP337-500 |
| Nonidet P40 substitute (Igepal CA-630) |
USB Corporation |
Cat#: 19628 |
| Triethylammonium bicarbonate (TEAB) buffer |
Sigma-Aldrich |
Cat#: T7408-500ML |
| TMT10plex Isobaric Label Reagent Set |
Thermo Scientific |
Cat#: 90406 |
| TMT16plex Isobaric Label Reagent Set |
Thermo Scientific |
Cat#: A44520
|
| Hydroxylamine solution |
Sigma-Aldrich |
Cat#: 467804-10ML |
| Formic acid, ~98%, for mass spectrometry |
Honeywell Fluka |
Cat#: 94318-250ML-F |
| Critical commercial assays |
| CellTiter-Glo® Luminescent Cell Viability Assay |
Promega |
Cat#: G7573 |
| Caspase-Glo® 3/7 Assay System |
Promega |
Cat#: G8093 |
| NEBNext Ultra II RNA Library Prep Kit for Illumina |
New England Biolabs |
Cat#: E7770 |
| RNeasy Mini Plus Kits |
QIAGEN |
Cat#: 74034 |
| eBioscience™ Fixable Viability Dye eFluor™ 780 |
Invitrogen |
Cat#: 65-0865-18; N/A |
| Deposited data |
| All raw proteomic data have been uploaded to PRIDE |
This study |
PXD029655 |
| All RNA-sequencing data have been uploaded to GEO |
This study |
GSE185373, GSE220185, GSE220845
|
| All uncropped gels have been uploaded to Mendeley Data |
This study |
DOI: 10.17632/r6t9f3n9wr.1
|
| Experimental models: Cell lines |
| 22Rv1 |
ATCC |
CRL-2505; RRID:CVCL_1045 |
| MCF7 |
ATCC |
HTB-22; RRID:CVCL_0031 |
| Ramos |
ATCC |
CRL-1596; RRID:CVCL_0597 |
| THP1 |
ATCC |
TIB-202; RRID:CVCL_0006 |
| HEK293T |
ATCC |
CRL-3216; RRID:CVCL_0063 |
| HEK293FT |
Thermo Scientific |
R70007; RRID:CVCL_6911 |
| KBM7 |
Georg Winter, CeMM, Vienna |
RRID:CVCL_A426 |
| HCT-116 |
ATCC |
CCL-247; RRID:CVCL_0291 |
| Panc 04.03 |
ATCC |
CRL-2555; RRID:CVCL_1636 |
| Panc 05.04 |
ATCC |
CRL-2557; RRID:CVCL_1637 |
| E.G7-Ova |
ATCC |
CRL-2113; RRID:CVCL_3505 |
| Oligonucleotides |
| sgDDX42_N_sense 5’-CACCGattcctaacaggtcagtcat |
This study |
N/A |
| sgDDX42_N_anti 5’-AAACatgactgacctgttaggaatC |
This study |
N/A |
| RepDDX42N_1_P_F 5’-gcgttacatagcatcgtacgcgtacgtgtttggcttattcctaacaggtcagtatgaccgagtacaagcccacg |
This study |
N/A |
| RepDDX42N_1_P_R 5’-agcattctagagcatcgtaCGCGTACGTGTTTGGtccagttcatggtgccaatgGAagatccgccgccacc |
This study |
N/A |
| DDX42_N_seqF 5’-gcccttggggctatacacttt |
This study |
N/A |
| DDX42_N_seqR 5’-ccagcactgatggcaaaacc |
This study |
N/A |
| sgPSME1_sense 5’-CACCGccagcccgaggcccaagcca |
This study |
N/A |
| sgPSME2_sense 5’ CACCGaaatccagagacttacctcc |
This study |
N/A |
| sgControl-AAVS1_sense 5’-caccgGGGGCCACTAGGGACAGGAT |
This study |
N/A |
| Recombinant DNA |
| pLenti3.3/TR |
Thermo Scientific |
A11144 |
| psPAX2.0 |
Addgene |
12260 |
| CMV VSV-G |
Addgene |
98286 |
| pLenti6.3 |
Thermo Scientific |
A11144 |
| pLEX304 |
Addgene |
25890 |
| Software and algorithms |
| PRISM Version 9.0.0 |
GraphPad |
https://www.graphpad.com/features
|
| MaxQuant (v2.0.3.1) |
N/A |
https://www.maxquant.org/
|
| Integrated Proteomics Pipeline (IP2) |
Integrated Proteomics Applications, Inc |
http://proteomicswiki.com/wiki/index.php/IP2
|
| FlowJo (v10.0.7) |
TreeStar Inc. |
https://www.flowjo.com/
|
| edgeR (v3.32.1) |
Robinson et al., 2010
|
https://bioconductor.org/packages/release/bioc/html/edgeR.html
|
| DESeq2 (v1.30.1) |
Love et al., 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| limma voom (v3.46.0) |
Law et al., 2014
|
https://bioconductor.org/packages/release/bioc/html/limma.html
|
| ImageJ |
NIH |
https://imagej.nih.gov/ij/download.html
|
| PyMOL (v2.5.2) |
Schrödinger |
https://pymol.org/2/
|
| Trim_galore (v0.6.4) |
Martin et al., 2011
|
https://github.com/FelixKrueger/TrimGalore
|
| STAR (v2.7.5) |
Dobin et al., 2013
|
https://github.com/alexdobin/STAR/
|
| samtools (v1.9) |
Danecek et al., 2021
|
http://www.htslib.org/
|
| bamCoverage (part of the Deeptools package; v3.3.1) |
Ramírez et al., 2016
|
https://deeptools.readthedocs.io/en/develop/index.html
|
| featureCounts (part of the subread package; v1.5.0) |
Liao et al., 2014
|
https://subread.sourceforge.net/
|
| ChimeraX |
Pettersen et al., 2021 |
https://www.cgl.ucsf.edu/chimerax/
|
| Glide |
Schrödinger |
https://www.schrodinger.com/products/glide
|
| cutadapt 3.4 |
Martin et al., 2011
|
https://cutadapt.readthedocs.io/en/v3.4/#
|
| rMATS (v4.1.1) |
Shen et al., 2014
|
https://rnaseq-mats.sourceforge.net/rmats4.1.1/index.html
|
| Branchpointer |
Signal et al., 2018
|
https://github.com/signalbash/branchpointer
|
| Skipper |
Boyle et al., 2022
|
https://github.com/YeoLab/skipper
|
| skewer |
Jiang et al., 2014
|
https://github.com/relipmoc/skewer
|
| fastp 0.11.5 |
Chen et al., 2018
|
https://github.com/OpenGene/fastp
|
| UMIcollaps |
Liu et al., 2019
|
https://github.com/Daniel-Liu-c0deb0t/UMICollapse
|
| Other |
|
|
|
