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d5l5x cell signaling  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc d5l5x cell signaling
    D5l5x Cell Signaling, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 31 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/d5l5x+cell+signaling/FANCD2+Rabbit+mAb/pm37909041-466-58-59
    Average 94 stars, based on 31 article reviews
    d5l5x cell signaling - by Bioz Stars, 2026-09
    94/100 stars

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    Virus:

    Article Title: Widespread BRCA1/2 -independent homologous recombination defects are caused by alterations in RNA-binding proteins
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2 Article ll OPEN ACCESS

    Article Title: Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2

    Recombinant:

    Article Title: Widespread BRCA1/2 -independent homologous recombination defects are caused by alterations in RNA-binding proteins
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2 Article ll OPEN ACCESS

    Article Title: Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2

    RNA sequencing:

    Article Title: Widespread BRCA1/2 -independent homologous recombination defects are caused by alterations in RNA-binding proteins
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2 Article ll OPEN ACCESS

    Article Title: Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2

    Transfection:

    Article Title: Widespread BRCA1/2 -independent homologous recombination defects are caused by alterations in RNA-binding proteins
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2 Article ll OPEN ACCESS

    Article Title: Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2

    GWAS:

    Article Title: Widespread BRCA1/2 -independent homologous recombination defects are caused by alterations in RNA-binding proteins
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2 Article ll OPEN ACCESS

    Article Title: Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2

    Multiple Displacement Amplification:

    Article Title: Widespread BRCA1/2 -independent homologous recombination defects are caused by alterations in RNA-binding proteins
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2 Article ll OPEN ACCESS

    Article Title: Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2

    Synthesized:

    Article Title: Widespread BRCA1/2 -independent homologous recombination defects are caused by alterations in RNA-binding proteins
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2 Article ll OPEN ACCESS

    Article Title: Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies gH2AX, clone JBW301 Millipore Sigma Cat# 05-636; RRID:AB_309864 SNRPB GeneTex Cat# GTX101883; RRID:AB_1951963 NBS1 GeneTex Cat# GTX70224; RRID:AB_372445 ERCC1, clone EPR7277 abcam Cat# ab129267; RRID:AB_11157618 Rad51, clone EPR4030(3)) abcam Cat# ab133534; RRID:AB_2722613 PRPF8 Bethyl Cat# A303-921A; RRID:AB_2620270 SF3B3 Bethyl Cat# A302-508A; RRID:AB_1966103 FANCA, Clone D1L2Z Cell Signaling Cat# 14657; RRID:AB_2798558 FANCD2, Clone D5L5X Cell Signaling Cat# 16323; RRID:AB_2798761 Actin, Clone 8H10D10 Cell Signaling Cat# 3700; RRID:AB_2242334 anti-Mouse HRP Cell Signaling Cat# 7076; RRID:AB_330924 anti-Rabbit HRP Cell Signaling Cat# 7074; RRID:AB_2099233 anti-Rabbit Alexa Fluor 488 ThermoFisher Cat# A32731; RRID:AB_2633280 anti-Mouse Alexa Fluor 488 ThermoFisher Cat# A-11029; RRID:AB_2534088 Streptavidin, Alexa Fluor 647 ThermoFisher Cat# S21374; RRID:AB_2336066 Bacterial and virus strains DH10B ThermoFisher Cat# 18297010 Chemicals, peptides, and recombinant proteins KOD HotStart Polymerase Sigma Cat# 71086 Pladienolide B Tocris Cat# 60709 Mirin Sigma Cat# M9948 BMN673 (Talazoparib) Selleck Cat# S7048 AZD2281 (Olaparib) Selleck Cat# S1060 EdU CarboSynth Cat# NE08701 Azide-PEG3-Biotin Sigma Cat# 762024 Critical commercial assays PrestoBlue ThermoFisher Cat# A-13262 Lipofectamine 3000 ThermoFisher Cat# L3000015 Deposited data RNAseq data following siRNA transfection This paper GEO: GSE153396 TCGA Pan-Cancer Atlas Data TCGA Consortium https://portal.gdc.cancer.gov ICGC Data ICGC https://dcc.icgc.org MicroRNA Targets miRDB http://mirdb.org GWAS data GWASdb v2 http://jjwanglab.org/gwasdb PRPF8 eCLIP Data ENCODE ENCODE: ENCFF582YLB, ENCFF160MVU Experimental models: Cell lines BT-549 ATCC Cat# HTB-122; RRID:CVCL_1092 MDA-MB-231 ATCC Cat# HTB-26; RRID:CVCL_0062 HCC1806 ATCC Cat# CRL-2335; RRID:CVCL_1258 HCC38 ATCC Cat# CRL-2314; RRID:CVCL_1267 U2OS ATCC Cat# HTB-96; RRID:CVCL_A4CF Oligonucleotides Tag1-M13F: 50-GGCAGACGTGCCTCACTC CCAGTCACGACGTTGTAAAACG-30 Sigma Custom synthesized (Continued on next page) e1 Cell Reports Medicine 4, 101255, November 21, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tag2-M13R: 50-CTGAGCTTGACGCATTGC TAGTGTCTCAAAATCTCTGATGTTAC-30 Sigma Custom synthesized Tag1: 50-GGCAGACGTGCCTCACTACT-30 Sigma Custom synthesized Tag2: 50-CTGAGCTTGACGCATTGCTA-30 Sigma Custom synthesized siRNAs Sigma See Table S3 Recombinant DNA pGIPZ shDDX3X-1 Dharmacon Cat# V3LHS_644473 pGIPZ shDDX3X-2 Dharmacon Cat# V2LHS_202531 pGIPZ shSF3B3-1 Dharmacon Cat# V3LHS_644840 pGIPZ shSF3B3-2 Dharmacon Cat# V2LHS_43924 pGIPZ shBRCA2-1 Dharmacon Cat# V2LHS_89238 pGIPZ shBRCA2-2 Dharmacon Cat# V2LHS_89237 pGIPZ shControl Dharmacon Cat# RHS5346 pCBASceI Addgene Cat# 26477 pDRGFP Addgene Cat# 26475 pCAG-EGFP Addgene Cat# 89684 pcDNA3.1-ccdB-TagRFP SNRPE WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPE c.208T>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF3 c.227C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.1186C>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBM15 c.2009C>T This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC WT This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.211G>A This Paper N/A pcDNA3.1-ccdB-TagRFP HNRNPC c.341C>T This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 WT This Paper N/A pcDNA3.1-ccdB-TagRFP LUC7L2 c.1205C>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX WT This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.462A>T This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.743A>G This Paper N/A pcDNA3.1-ccdB-TagRFP RBMX c.760G>C This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 WT This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.18G>A This Paper N/A pcDNA3.1-ccdB-TagRFP PRPF31 c.456T>A This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 WT This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.169G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.57C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SF3B5 c.7G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 WT This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.10G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.349G>A This Paper N/A pcDNA3.1-ccdB-TagRFP CDC73 c.729G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB WT This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.18C>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.247G>T This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.249G>C This Paper N/A pcDNA3.1-ccdB-TagRFP SNRPB c.35A>G This Paper N/A (Continued on next page) Cell Reports Medicine 4, 101255, November 21, 2023 e2



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