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    ATCC mda-mb-231
    Mda Mb 231, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 3682 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/mda+mb/MDA-MB-231/custom%40crm-htb-26%4042472092
    Average 99 stars, based on 3682 article reviews
    mda-mb-231 - by Bioz Stars, 2026-09
    99/100 stars

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    Cell Culture:

    Article Title: Hypoxia-reoxygenation cycle leads to context dependent phenotypic effects in breast cancer cell lines.
    Article Snippet: 1 Hypoxia and Clinical Genomics Laboratory (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India 2 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India 3 Medical Oncology, Tata Memorial Centre, Director’s Office, Ground Floor, Main Building, Tata Memorial Hospital, E. Borges Road, Parel, Mumbai 400012, Maharashtra, India 4 Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, Maharashtra, India Abstract Background Hypoxia is a common feature of solid tumors and is associated with cancer progression.. We investigated the effect of hypoxia followed by reoxygenation on the phenotypic behavior of two breast cancer cell lines, MCF-7 and MDA-MB-231.. Methods and Results MCF-7 and MDA-MB-231 cells were exposed to controlled hypoxia (1% O2, 1 h and 24 h) followed by reoxygenation (24 h to 96 h) and compared to their normoxic controls for cell proliferation, survival, migration and invasion, and chemoresistance.

    Multiple Displacement Amplification:

    Article Title: Hypoxia-reoxygenation cycle leads to context dependent phenotypic effects in breast cancer cell lines.
    Article Snippet: 1 Hypoxia and Clinical Genomics Laboratory (Clinician Scientist Laboratory), Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra 410210, India 2 Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India 3 Medical Oncology, Tata Memorial Centre, Director’s Office, Ground Floor, Main Building, Tata Memorial Hospital, E. Borges Road, Parel, Mumbai 400012, Maharashtra, India 4 Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, Maharashtra, India Abstract Background Hypoxia is a common feature of solid tumors and is associated with cancer progression.. We investigated the effect of hypoxia followed by reoxygenation on the phenotypic behavior of two breast cancer cell lines, MCF-7 and MDA-MB-231.. Methods and Results MCF-7 and MDA-MB-231 cells were exposed to controlled hypoxia (1% O2, 1 h and 24 h) followed by reoxygenation (24 h to 96 h) and compared to their normoxic controls for cell proliferation, survival, migration and invasion, and chemoresistance.

    Article Title: Conjugation chemistry for catalytic antibody 38C2
    Article Snippet: .. Human breast cancer cell lines SK-BR-3 and MDA-MB-231 were purchased from ATCC. ..

    Article Title: Spatiotemporally programmed nanomedicine engineering to resolve conflicting immunosignals in triple-negative breast cancer.
    Article Snippet: .. Cell lines source was as follows: 4T1, B16, CT26, and MDA-MB-231 were purchased from the American Type Culture Collection (ATCC, VA, USA); SW620 and HT29 were from Procell Life Science & Technology (Wuhan, China). ..

    Article Title: Essential lncRNAs in the human transcriptome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-HA peptide antibody Cell Signaling Technology Cat# 2367S; RRID: AB_10691311 Anti-H3k27ac antibody Active Motif Cat# 39133; RRID: AB_2561016 Bacterial and virus strains NEB Stable Cells New England Biolabs Cat# C3040I Endura Electrocompetent Cells Lucigen Cat# 60242–2 Chemicals, peptides, and recombinant proteins Polyethyleneimine Polysciences Cat# 23966 Puromycin Invivogen Cat# ant-pr-1 Blasticidin S A.G. Scientific Cat# B-1247-SOL Doxycycline Sigma-Aldrich Cat# D3447 Doxorubicin MedChemExpress Cat# HY-15142 Dinaciclib MedChemExpress Cat# HY-10492 Critical commercial assays KAPA Total RNA-seq kit with RiboErase Roche Cat# 07962282001 Stranded mRNA Prep Illumina Cat# 20040532 RNA UD Indexes, Set A Illumina Cat# 20040553 Chromium Single Cell 3′ Gene Expression v3.1 with feature barcoding technology for CRISPR screening 10x Genomics Cat# 10000127, 10000268 and 10000262 TaqB polymerase Enzymatics Cat# P7250L 2× Rapid Ligase Buffer Enzymatics Cat# B1010L Q5 High-Fidelity DNA Polymerase NEB Cat# M0491 T7 DNA Ligase NEB Cat# M0318L T4 DNA Ligase NEB Cat# B0202S Gibson Assembly Master Mix NEB Cat# E2611L KAPA HiFi HotStart ReadyMix PCR Kit Roche Cat# 07958935001 SPRI beads Beckman Cat# B23317 MAXI Fast-Ion Plasmid Purification Kit IBI Scientific Cat# IB47125 QIAGEN Plasmid Mini Kit Qiagen Cat# 12123 QiaQuick Gel Extraction Kit Qiagen Cat# 28704 DNA Clean & Concentrator Zymo Cat# D4014 Qubit RNA XR Assay Kit Thermo Cat# Q10210 Qubit dsDNA HS Assay Kit Thermo Cat# Q32851 FastDigest Esp3I Thermo Cat# FD0454 FastDigest LguI Thermo Cat# FD1934 FastDigest NheI Thermo Cat# FD0974 FastDigest ApaI Thermo Cat# FD1414 FastDigest BamHI Thermo Cat# FD0055 FastDigest KpnI Thermo Cat# FD0524 FastAP Thermosensitive Alkaline Phosphatase Thermo Cat# EF0651 Qubit RNA XR Assay Kit Thermo Cat# Q10210 MboI NEB Cat# R0147M DNA Polymerase I Large (Klenow) Fragment NEB Cat# M0210L (Continued on next page) e1 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-14-dATP Thermo Cat# 19524016 Direct-zol RNA Purification Kit Zymo Cat# R2062 Agilent High Sensitivity DNA Kit Agilent Cat# 5067–4626 RevertAid Reverse Transcriptase Thermo Cat# EP0442 Luna Universal qPCR Master Mix NEB Cat# M3003E Lipofectamine RNAiMAX Thermo Cat# 13778075 LIVE/DEAD Fixable Violet Dead Cell Stain Kit Thermo Cat# L34963 Incucyte Annexin V Dye for Apoptosis Sartorius Cat# 4642 Proteinase K NEB Cat# P8107S RNase A A.G.Scientific Cat# R-2000 TE Buffer Sigma Cat# 93283 Dynabeads Protein A Thermo Cat# 10001D Dynabeads M-280 Streptavidin Thermo Cat# 11205D Deposited data MDA-MB-231 total RNA-seq fastq RNA atlas76 N/A Developmental lncRNA annotation (human.lncRNA.gtf) Sarropoulos et al.19 N/A Developmental samples Sarropoulos et al.19 and Cardoso-Moreira et al.52 N/A Fastq files of TCGA RNA-seq samples TCGA, dbGaP (phs000178.v11.p8) https://portal.gdc.cancer.gov/, https:// www.ncbi.nlm.nih.gov/projects/gap/cgibin/study.cgi?study_id=phs000178.v11.p8 GRCh38 reference genome (GRCh38.d1.vd1.fa.tar) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files GENCODE v36 (gencode.v36.annotation.gtf.gz) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files 10x Genomics reference (refdata-gexGRCh38-2024-A) 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads HISAT2 indexes (UCSC hg38) HISAT2 https://daehwankimlab.github.io/hisat2/ download/ K562 and KBM7 Hi-C TADs bed files (TADs in hg38) Hi-C genome Browser77 http://3dgenome.fsm.northwestern.edu/ publications.html) Pooled transcriptome-scale RNA-targeting Cas13 screens This study BioProject: PRJNA1344834 Total RNA-seq of parental and Cas13engineered cells This study BioProject: PRJNA1344834 Stranded RNA-seq with polyA-enrichment of Cas13-engineered cells This study BioProject: PRJNA1344834 CaRPool-seq of MDA-MB-231 and HAP1 perturbed cells This study BioProject: PRJNA1344834 mRNA-seq of MDA-MB-231 perturbed cells This study BioProject: PRJNA1344834 H3K27ac AQuA-HiChIP of HAP1 cells This study BioProject: PRJNA1344834 Experimental models: Cell lines HAP1 Guo et al.24 N/A HEK293FT Thermo Cat# R70007 K562 ATCC Cat# CCL-243 MDA-MB-231 ATCC Cat# HTB-26 THP1 Wessels and Méndez-Mancilla et al.48 N/A HAP1 RfxCas13d Guo et al.24 N/A HEK293FT RfxCas13d Wessels and Méndez-Mancilla et al.23 N/A (Continued on next page) Cell Genomics 6, 101253, July 8, 2026 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER K562 RfxCas13d This study N/A MDA-MB-231 RfxCas13d This study N/A THP1 RfxCas13d Wessels and Méndez-Mancilla et al.48 N/A Oligonucleotides Guide RNA sequences, see Tables S1B, S3A, and S4A This study N/A lncRNA-targeting siRNA sequences, see Table S3D This study N/A RT-qPCR oligo sequences, see Table S3B This study N/A Recombinant DNA pLentiRNACRISPR_007 - TetO-NLSRfxCas13d- NLS-WPRE-EFS-rtTA3-2ABlast Wessels and Méndez-Mancilla et al.23 Addgene 138149 pLentiRNAGuide_001 - hU6-RfxCas13dDR1- BsmBI-EFS-Puro-WPRE Wessels and Méndez-Mancilla et al.23 Addgene 138150 pLentiRNAGuide_004 - hU6-RfxCas13dDR1- EGFP-P2A-PuroR Hart et al.34 Addgene 223175 tFUCCI(CA)5 Ando et al.43 Addgene 153521 pLentiFUCCI(CA)5 This study Addgene 223176 pMD2.G Didier Trono Addgene 12259 psPAX2 Didier Trono Addgene 12260 Software and algorithms Cas13 design tool Guo et al.24 https://cas13design.nygenome.org/ Cas13 guide design algorithm Wessels and Méndez-Mancilla et al.23 https://gitlab.com/sanjanalab/cas13 TIGER gRNA design Wessels and Stirn et al.78 https://tiger.nygenome.org/ Cutadapt v.1.13 Martin79 https://cutadapt.readthedocs.io/en/stable/ Bowtie v.1.1.2 Langmead et al.80 https://bowtie-bio.sourceforge.net/index. shtml SVA v.3.34.0 Leek et al.81 https://bioconductor.org/packages/ release/bioc/html/sva.html RobustRankAggreg v1.2.1 Kolde et al.82 https://cran.r-project.org/web/packages/ RobustRankAggreg/index.html STAR Dobin et al.83 https://github.com/alexdobin/STAR RSEM Li and Dewey84 https://github.com/deweylab/RSEM Tximport Soneson et al.85 https://bioconductor.org/packages/ release/bioc/html/tximport.html DESeq2 v.3.19 Love et al.86 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html survival v.3.2.7 Therneau et al.87,88 https://CRAN.R-project.org/ package=survival survminer v.0.4.9 Kassambara et al.89 https://rpkgs.datanovia.com/survminer/ index.html clusterProfiler v4.10.0 Yu et al.90 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html MSigDB v2023.2 Subramanian et al. https://www.gsea-msigdb.org/gsea/ msigdb/collections.jsp 10x Genomics Cell Ranger v9.0.0 Zheng et al.91 https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat v4.1.1 Hao et al.92 https://satijalab.org/seurat/ FeatureCounts v2.0.4 Liao et al.93 https://subread.sourceforge.net/ featureCounts.html (Continued on next page) e3 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS

    Article Title: Isolated recombinant oncolytic adenoviruses, pharmaceutical compositions, and uses thereof for drugs for treatment of tumors and/or cancers
    Article Snippet: .. Cells AD293, MRC-5, Hela, A549, U251, HCT116, PANC1, HT29, H460, MDA-MB-231 were purchased from ATCC; HUVEC was purchased from Allcells Biotechnology (Shanghai) Co., Ltd. 2. .. Oncolytic adenovirus H101 was purchased from Shanghai Sunway Biotech Co., Ltd. 3.

    Article Title: Sparingly PEGylated Adipate Copolymers via Enzymatic Synthesis as Nano-Carriers for Solid Dispersions.
    Article Snippet: .. The human epithelial cell line Caco-2, the MCF-7 human breast cancer cells, and the MDA-MB-231 late-stage triple-negative breast cancer cells were obtained from the American Type Culture Collection (ATCC) and used across a 10-passage window. ..

    Article Title: Ethanolic extract of Otostegia fruticosa induces ROS-dependent apoptosis and reduces migration of MDA-MB-231 cells in vitro
    Article Snippet: Primary antibodies (Caspase-9 (#9502) (1:1000 μL), BCL2 (#3498) (1:1000 μL), Cyt-c (#11940) (1:1000 μL), MMP-9 (#3852) (1:1000 μL), OPN (#88742) (1:1000 μL), pAkt (#9271) (1:1000 μL), and Actin B (#4967) (1:2000 μL)) and Secondary antibody (#7056 & #7054/1:5000 μL) utilized in western blot analysis were obtained from Cell Signaling Technology (USA). .. The MDA-MB-231 human breast cancer cell line was obtained from the American Type Culture Collection (ATCC-HTB-26, USA). .. Cells were cultured in a humidified atmosphere at 37°C with 5% CO 2 , using Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic mixture (streptomycin and penicillin) (Invitrogen, Carlsbad, CA, USA).

    Article Title: Noncanonical PI(4,5)P 2 coordinates lysosome positioning through cholesterol trafficking
    Article Snippet: MEFs, HEK293A, HEK293T, MCF-7, MDA-MB-436, and HCC1806 cells were cultured in DMEM (10-013-CV, Corning) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin (100 U/ml) (15140122, Thermo Fisher Scientific). .. HEK293T, HEK293A, MCF-7, HCC1806, and MDA-MB-436 were obtained from the American Type Culture Collection. ..

    Purification:

    Article Title: Essential lncRNAs in the human transcriptome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-HA peptide antibody Cell Signaling Technology Cat# 2367S; RRID: AB_10691311 Anti-H3k27ac antibody Active Motif Cat# 39133; RRID: AB_2561016 Bacterial and virus strains NEB Stable Cells New England Biolabs Cat# C3040I Endura Electrocompetent Cells Lucigen Cat# 60242–2 Chemicals, peptides, and recombinant proteins Polyethyleneimine Polysciences Cat# 23966 Puromycin Invivogen Cat# ant-pr-1 Blasticidin S A.G. Scientific Cat# B-1247-SOL Doxycycline Sigma-Aldrich Cat# D3447 Doxorubicin MedChemExpress Cat# HY-15142 Dinaciclib MedChemExpress Cat# HY-10492 Critical commercial assays KAPA Total RNA-seq kit with RiboErase Roche Cat# 07962282001 Stranded mRNA Prep Illumina Cat# 20040532 RNA UD Indexes, Set A Illumina Cat# 20040553 Chromium Single Cell 3′ Gene Expression v3.1 with feature barcoding technology for CRISPR screening 10x Genomics Cat# 10000127, 10000268 and 10000262 TaqB polymerase Enzymatics Cat# P7250L 2× Rapid Ligase Buffer Enzymatics Cat# B1010L Q5 High-Fidelity DNA Polymerase NEB Cat# M0491 T7 DNA Ligase NEB Cat# M0318L T4 DNA Ligase NEB Cat# B0202S Gibson Assembly Master Mix NEB Cat# E2611L KAPA HiFi HotStart ReadyMix PCR Kit Roche Cat# 07958935001 SPRI beads Beckman Cat# B23317 MAXI Fast-Ion Plasmid Purification Kit IBI Scientific Cat# IB47125 QIAGEN Plasmid Mini Kit Qiagen Cat# 12123 QiaQuick Gel Extraction Kit Qiagen Cat# 28704 DNA Clean & Concentrator Zymo Cat# D4014 Qubit RNA XR Assay Kit Thermo Cat# Q10210 Qubit dsDNA HS Assay Kit Thermo Cat# Q32851 FastDigest Esp3I Thermo Cat# FD0454 FastDigest LguI Thermo Cat# FD1934 FastDigest NheI Thermo Cat# FD0974 FastDigest ApaI Thermo Cat# FD1414 FastDigest BamHI Thermo Cat# FD0055 FastDigest KpnI Thermo Cat# FD0524 FastAP Thermosensitive Alkaline Phosphatase Thermo Cat# EF0651 Qubit RNA XR Assay Kit Thermo Cat# Q10210 MboI NEB Cat# R0147M DNA Polymerase I Large (Klenow) Fragment NEB Cat# M0210L (Continued on next page) e1 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-14-dATP Thermo Cat# 19524016 Direct-zol RNA Purification Kit Zymo Cat# R2062 Agilent High Sensitivity DNA Kit Agilent Cat# 5067–4626 RevertAid Reverse Transcriptase Thermo Cat# EP0442 Luna Universal qPCR Master Mix NEB Cat# M3003E Lipofectamine RNAiMAX Thermo Cat# 13778075 LIVE/DEAD Fixable Violet Dead Cell Stain Kit Thermo Cat# L34963 Incucyte Annexin V Dye for Apoptosis Sartorius Cat# 4642 Proteinase K NEB Cat# P8107S RNase A A.G.Scientific Cat# R-2000 TE Buffer Sigma Cat# 93283 Dynabeads Protein A Thermo Cat# 10001D Dynabeads M-280 Streptavidin Thermo Cat# 11205D Deposited data MDA-MB-231 total RNA-seq fastq RNA atlas76 N/A Developmental lncRNA annotation (human.lncRNA.gtf) Sarropoulos et al.19 N/A Developmental samples Sarropoulos et al.19 and Cardoso-Moreira et al.52 N/A Fastq files of TCGA RNA-seq samples TCGA, dbGaP (phs000178.v11.p8) https://portal.gdc.cancer.gov/, https:// www.ncbi.nlm.nih.gov/projects/gap/cgibin/study.cgi?study_id=phs000178.v11.p8 GRCh38 reference genome (GRCh38.d1.vd1.fa.tar) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files GENCODE v36 (gencode.v36.annotation.gtf.gz) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files 10x Genomics reference (refdata-gexGRCh38-2024-A) 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads HISAT2 indexes (UCSC hg38) HISAT2 https://daehwankimlab.github.io/hisat2/ download/ K562 and KBM7 Hi-C TADs bed files (TADs in hg38) Hi-C genome Browser77 http://3dgenome.fsm.northwestern.edu/ publications.html) Pooled transcriptome-scale RNA-targeting Cas13 screens This study BioProject: PRJNA1344834 Total RNA-seq of parental and Cas13engineered cells This study BioProject: PRJNA1344834 Stranded RNA-seq with polyA-enrichment of Cas13-engineered cells This study BioProject: PRJNA1344834 CaRPool-seq of MDA-MB-231 and HAP1 perturbed cells This study BioProject: PRJNA1344834 mRNA-seq of MDA-MB-231 perturbed cells This study BioProject: PRJNA1344834 H3K27ac AQuA-HiChIP of HAP1 cells This study BioProject: PRJNA1344834 Experimental models: Cell lines HAP1 Guo et al.24 N/A HEK293FT Thermo Cat# R70007 K562 ATCC Cat# CCL-243 MDA-MB-231 ATCC Cat# HTB-26 THP1 Wessels and Méndez-Mancilla et al.48 N/A HAP1 RfxCas13d Guo et al.24 N/A HEK293FT RfxCas13d Wessels and Méndez-Mancilla et al.23 N/A (Continued on next page) Cell Genomics 6, 101253, July 8, 2026 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER K562 RfxCas13d This study N/A MDA-MB-231 RfxCas13d This study N/A THP1 RfxCas13d Wessels and Méndez-Mancilla et al.48 N/A Oligonucleotides Guide RNA sequences, see Tables S1B, S3A, and S4A This study N/A lncRNA-targeting siRNA sequences, see Table S3D This study N/A RT-qPCR oligo sequences, see Table S3B This study N/A Recombinant DNA pLentiRNACRISPR_007 - TetO-NLSRfxCas13d- NLS-WPRE-EFS-rtTA3-2ABlast Wessels and Méndez-Mancilla et al.23 Addgene 138149 pLentiRNAGuide_001 - hU6-RfxCas13dDR1- BsmBI-EFS-Puro-WPRE Wessels and Méndez-Mancilla et al.23 Addgene 138150 pLentiRNAGuide_004 - hU6-RfxCas13dDR1- EGFP-P2A-PuroR Hart et al.34 Addgene 223175 tFUCCI(CA)5 Ando et al.43 Addgene 153521 pLentiFUCCI(CA)5 This study Addgene 223176 pMD2.G Didier Trono Addgene 12259 psPAX2 Didier Trono Addgene 12260 Software and algorithms Cas13 design tool Guo et al.24 https://cas13design.nygenome.org/ Cas13 guide design algorithm Wessels and Méndez-Mancilla et al.23 https://gitlab.com/sanjanalab/cas13 TIGER gRNA design Wessels and Stirn et al.78 https://tiger.nygenome.org/ Cutadapt v.1.13 Martin79 https://cutadapt.readthedocs.io/en/stable/ Bowtie v.1.1.2 Langmead et al.80 https://bowtie-bio.sourceforge.net/index. shtml SVA v.3.34.0 Leek et al.81 https://bioconductor.org/packages/ release/bioc/html/sva.html RobustRankAggreg v1.2.1 Kolde et al.82 https://cran.r-project.org/web/packages/ RobustRankAggreg/index.html STAR Dobin et al.83 https://github.com/alexdobin/STAR RSEM Li and Dewey84 https://github.com/deweylab/RSEM Tximport Soneson et al.85 https://bioconductor.org/packages/ release/bioc/html/tximport.html DESeq2 v.3.19 Love et al.86 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html survival v.3.2.7 Therneau et al.87,88 https://CRAN.R-project.org/ package=survival survminer v.0.4.9 Kassambara et al.89 https://rpkgs.datanovia.com/survminer/ index.html clusterProfiler v4.10.0 Yu et al.90 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html MSigDB v2023.2 Subramanian et al. https://www.gsea-msigdb.org/gsea/ msigdb/collections.jsp 10x Genomics Cell Ranger v9.0.0 Zheng et al.91 https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat v4.1.1 Hao et al.92 https://satijalab.org/seurat/ FeatureCounts v2.0.4 Liao et al.93 https://subread.sourceforge.net/ featureCounts.html (Continued on next page) e3 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS

    Reverse Transcription:

    Article Title: Essential lncRNAs in the human transcriptome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-HA peptide antibody Cell Signaling Technology Cat# 2367S; RRID: AB_10691311 Anti-H3k27ac antibody Active Motif Cat# 39133; RRID: AB_2561016 Bacterial and virus strains NEB Stable Cells New England Biolabs Cat# C3040I Endura Electrocompetent Cells Lucigen Cat# 60242–2 Chemicals, peptides, and recombinant proteins Polyethyleneimine Polysciences Cat# 23966 Puromycin Invivogen Cat# ant-pr-1 Blasticidin S A.G. Scientific Cat# B-1247-SOL Doxycycline Sigma-Aldrich Cat# D3447 Doxorubicin MedChemExpress Cat# HY-15142 Dinaciclib MedChemExpress Cat# HY-10492 Critical commercial assays KAPA Total RNA-seq kit with RiboErase Roche Cat# 07962282001 Stranded mRNA Prep Illumina Cat# 20040532 RNA UD Indexes, Set A Illumina Cat# 20040553 Chromium Single Cell 3′ Gene Expression v3.1 with feature barcoding technology for CRISPR screening 10x Genomics Cat# 10000127, 10000268 and 10000262 TaqB polymerase Enzymatics Cat# P7250L 2× Rapid Ligase Buffer Enzymatics Cat# B1010L Q5 High-Fidelity DNA Polymerase NEB Cat# M0491 T7 DNA Ligase NEB Cat# M0318L T4 DNA Ligase NEB Cat# B0202S Gibson Assembly Master Mix NEB Cat# E2611L KAPA HiFi HotStart ReadyMix PCR Kit Roche Cat# 07958935001 SPRI beads Beckman Cat# B23317 MAXI Fast-Ion Plasmid Purification Kit IBI Scientific Cat# IB47125 QIAGEN Plasmid Mini Kit Qiagen Cat# 12123 QiaQuick Gel Extraction Kit Qiagen Cat# 28704 DNA Clean & Concentrator Zymo Cat# D4014 Qubit RNA XR Assay Kit Thermo Cat# Q10210 Qubit dsDNA HS Assay Kit Thermo Cat# Q32851 FastDigest Esp3I Thermo Cat# FD0454 FastDigest LguI Thermo Cat# FD1934 FastDigest NheI Thermo Cat# FD0974 FastDigest ApaI Thermo Cat# FD1414 FastDigest BamHI Thermo Cat# FD0055 FastDigest KpnI Thermo Cat# FD0524 FastAP Thermosensitive Alkaline Phosphatase Thermo Cat# EF0651 Qubit RNA XR Assay Kit Thermo Cat# Q10210 MboI NEB Cat# R0147M DNA Polymerase I Large (Klenow) Fragment NEB Cat# M0210L (Continued on next page) e1 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-14-dATP Thermo Cat# 19524016 Direct-zol RNA Purification Kit Zymo Cat# R2062 Agilent High Sensitivity DNA Kit Agilent Cat# 5067–4626 RevertAid Reverse Transcriptase Thermo Cat# EP0442 Luna Universal qPCR Master Mix NEB Cat# M3003E Lipofectamine RNAiMAX Thermo Cat# 13778075 LIVE/DEAD Fixable Violet Dead Cell Stain Kit Thermo Cat# L34963 Incucyte Annexin V Dye for Apoptosis Sartorius Cat# 4642 Proteinase K NEB Cat# P8107S RNase A A.G.Scientific Cat# R-2000 TE Buffer Sigma Cat# 93283 Dynabeads Protein A Thermo Cat# 10001D Dynabeads M-280 Streptavidin Thermo Cat# 11205D Deposited data MDA-MB-231 total RNA-seq fastq RNA atlas76 N/A Developmental lncRNA annotation (human.lncRNA.gtf) Sarropoulos et al.19 N/A Developmental samples Sarropoulos et al.19 and Cardoso-Moreira et al.52 N/A Fastq files of TCGA RNA-seq samples TCGA, dbGaP (phs000178.v11.p8) https://portal.gdc.cancer.gov/, https:// www.ncbi.nlm.nih.gov/projects/gap/cgibin/study.cgi?study_id=phs000178.v11.p8 GRCh38 reference genome (GRCh38.d1.vd1.fa.tar) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files GENCODE v36 (gencode.v36.annotation.gtf.gz) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files 10x Genomics reference (refdata-gexGRCh38-2024-A) 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads HISAT2 indexes (UCSC hg38) HISAT2 https://daehwankimlab.github.io/hisat2/ download/ K562 and KBM7 Hi-C TADs bed files (TADs in hg38) Hi-C genome Browser77 http://3dgenome.fsm.northwestern.edu/ publications.html) Pooled transcriptome-scale RNA-targeting Cas13 screens This study BioProject: PRJNA1344834 Total RNA-seq of parental and Cas13engineered cells This study BioProject: PRJNA1344834 Stranded RNA-seq with polyA-enrichment of Cas13-engineered cells This study BioProject: PRJNA1344834 CaRPool-seq of MDA-MB-231 and HAP1 perturbed cells This study BioProject: PRJNA1344834 mRNA-seq of MDA-MB-231 perturbed cells This study BioProject: PRJNA1344834 H3K27ac AQuA-HiChIP of HAP1 cells This study BioProject: PRJNA1344834 Experimental models: Cell lines HAP1 Guo et al.24 N/A HEK293FT Thermo Cat# R70007 K562 ATCC Cat# CCL-243 MDA-MB-231 ATCC Cat# HTB-26 THP1 Wessels and Méndez-Mancilla et al.48 N/A HAP1 RfxCas13d Guo et al.24 N/A HEK293FT RfxCas13d Wessels and Méndez-Mancilla et al.23 N/A (Continued on next page) Cell Genomics 6, 101253, July 8, 2026 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER K562 RfxCas13d This study N/A MDA-MB-231 RfxCas13d This study N/A THP1 RfxCas13d Wessels and Méndez-Mancilla et al.48 N/A Oligonucleotides Guide RNA sequences, see Tables S1B, S3A, and S4A This study N/A lncRNA-targeting siRNA sequences, see Table S3D This study N/A RT-qPCR oligo sequences, see Table S3B This study N/A Recombinant DNA pLentiRNACRISPR_007 - TetO-NLSRfxCas13d- NLS-WPRE-EFS-rtTA3-2ABlast Wessels and Méndez-Mancilla et al.23 Addgene 138149 pLentiRNAGuide_001 - hU6-RfxCas13dDR1- BsmBI-EFS-Puro-WPRE Wessels and Méndez-Mancilla et al.23 Addgene 138150 pLentiRNAGuide_004 - hU6-RfxCas13dDR1- EGFP-P2A-PuroR Hart et al.34 Addgene 223175 tFUCCI(CA)5 Ando et al.43 Addgene 153521 pLentiFUCCI(CA)5 This study Addgene 223176 pMD2.G Didier Trono Addgene 12259 psPAX2 Didier Trono Addgene 12260 Software and algorithms Cas13 design tool Guo et al.24 https://cas13design.nygenome.org/ Cas13 guide design algorithm Wessels and Méndez-Mancilla et al.23 https://gitlab.com/sanjanalab/cas13 TIGER gRNA design Wessels and Stirn et al.78 https://tiger.nygenome.org/ Cutadapt v.1.13 Martin79 https://cutadapt.readthedocs.io/en/stable/ Bowtie v.1.1.2 Langmead et al.80 https://bowtie-bio.sourceforge.net/index. shtml SVA v.3.34.0 Leek et al.81 https://bioconductor.org/packages/ release/bioc/html/sva.html RobustRankAggreg v1.2.1 Kolde et al.82 https://cran.r-project.org/web/packages/ RobustRankAggreg/index.html STAR Dobin et al.83 https://github.com/alexdobin/STAR RSEM Li and Dewey84 https://github.com/deweylab/RSEM Tximport Soneson et al.85 https://bioconductor.org/packages/ release/bioc/html/tximport.html DESeq2 v.3.19 Love et al.86 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html survival v.3.2.7 Therneau et al.87,88 https://CRAN.R-project.org/ package=survival survminer v.0.4.9 Kassambara et al.89 https://rpkgs.datanovia.com/survminer/ index.html clusterProfiler v4.10.0 Yu et al.90 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html MSigDB v2023.2 Subramanian et al. https://www.gsea-msigdb.org/gsea/ msigdb/collections.jsp 10x Genomics Cell Ranger v9.0.0 Zheng et al.91 https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat v4.1.1 Hao et al.92 https://satijalab.org/seurat/ FeatureCounts v2.0.4 Liao et al.93 https://subread.sourceforge.net/ featureCounts.html (Continued on next page) e3 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS

    Real-time Polymerase Chain Reaction:

    Article Title: Essential lncRNAs in the human transcriptome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-HA peptide antibody Cell Signaling Technology Cat# 2367S; RRID: AB_10691311 Anti-H3k27ac antibody Active Motif Cat# 39133; RRID: AB_2561016 Bacterial and virus strains NEB Stable Cells New England Biolabs Cat# C3040I Endura Electrocompetent Cells Lucigen Cat# 60242–2 Chemicals, peptides, and recombinant proteins Polyethyleneimine Polysciences Cat# 23966 Puromycin Invivogen Cat# ant-pr-1 Blasticidin S A.G. Scientific Cat# B-1247-SOL Doxycycline Sigma-Aldrich Cat# D3447 Doxorubicin MedChemExpress Cat# HY-15142 Dinaciclib MedChemExpress Cat# HY-10492 Critical commercial assays KAPA Total RNA-seq kit with RiboErase Roche Cat# 07962282001 Stranded mRNA Prep Illumina Cat# 20040532 RNA UD Indexes, Set A Illumina Cat# 20040553 Chromium Single Cell 3′ Gene Expression v3.1 with feature barcoding technology for CRISPR screening 10x Genomics Cat# 10000127, 10000268 and 10000262 TaqB polymerase Enzymatics Cat# P7250L 2× Rapid Ligase Buffer Enzymatics Cat# B1010L Q5 High-Fidelity DNA Polymerase NEB Cat# M0491 T7 DNA Ligase NEB Cat# M0318L T4 DNA Ligase NEB Cat# B0202S Gibson Assembly Master Mix NEB Cat# E2611L KAPA HiFi HotStart ReadyMix PCR Kit Roche Cat# 07958935001 SPRI beads Beckman Cat# B23317 MAXI Fast-Ion Plasmid Purification Kit IBI Scientific Cat# IB47125 QIAGEN Plasmid Mini Kit Qiagen Cat# 12123 QiaQuick Gel Extraction Kit Qiagen Cat# 28704 DNA Clean & Concentrator Zymo Cat# D4014 Qubit RNA XR Assay Kit Thermo Cat# Q10210 Qubit dsDNA HS Assay Kit Thermo Cat# Q32851 FastDigest Esp3I Thermo Cat# FD0454 FastDigest LguI Thermo Cat# FD1934 FastDigest NheI Thermo Cat# FD0974 FastDigest ApaI Thermo Cat# FD1414 FastDigest BamHI Thermo Cat# FD0055 FastDigest KpnI Thermo Cat# FD0524 FastAP Thermosensitive Alkaline Phosphatase Thermo Cat# EF0651 Qubit RNA XR Assay Kit Thermo Cat# Q10210 MboI NEB Cat# R0147M DNA Polymerase I Large (Klenow) Fragment NEB Cat# M0210L (Continued on next page) e1 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-14-dATP Thermo Cat# 19524016 Direct-zol RNA Purification Kit Zymo Cat# R2062 Agilent High Sensitivity DNA Kit Agilent Cat# 5067–4626 RevertAid Reverse Transcriptase Thermo Cat# EP0442 Luna Universal qPCR Master Mix NEB Cat# M3003E Lipofectamine RNAiMAX Thermo Cat# 13778075 LIVE/DEAD Fixable Violet Dead Cell Stain Kit Thermo Cat# L34963 Incucyte Annexin V Dye for Apoptosis Sartorius Cat# 4642 Proteinase K NEB Cat# P8107S RNase A A.G.Scientific Cat# R-2000 TE Buffer Sigma Cat# 93283 Dynabeads Protein A Thermo Cat# 10001D Dynabeads M-280 Streptavidin Thermo Cat# 11205D Deposited data MDA-MB-231 total RNA-seq fastq RNA atlas76 N/A Developmental lncRNA annotation (human.lncRNA.gtf) Sarropoulos et al.19 N/A Developmental samples Sarropoulos et al.19 and Cardoso-Moreira et al.52 N/A Fastq files of TCGA RNA-seq samples TCGA, dbGaP (phs000178.v11.p8) https://portal.gdc.cancer.gov/, https:// www.ncbi.nlm.nih.gov/projects/gap/cgibin/study.cgi?study_id=phs000178.v11.p8 GRCh38 reference genome (GRCh38.d1.vd1.fa.tar) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files GENCODE v36 (gencode.v36.annotation.gtf.gz) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files 10x Genomics reference (refdata-gexGRCh38-2024-A) 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads HISAT2 indexes (UCSC hg38) HISAT2 https://daehwankimlab.github.io/hisat2/ download/ K562 and KBM7 Hi-C TADs bed files (TADs in hg38) Hi-C genome Browser77 http://3dgenome.fsm.northwestern.edu/ publications.html) Pooled transcriptome-scale RNA-targeting Cas13 screens This study BioProject: PRJNA1344834 Total RNA-seq of parental and Cas13engineered cells This study BioProject: PRJNA1344834 Stranded RNA-seq with polyA-enrichment of Cas13-engineered cells This study BioProject: PRJNA1344834 CaRPool-seq of MDA-MB-231 and HAP1 perturbed cells This study BioProject: PRJNA1344834 mRNA-seq of MDA-MB-231 perturbed cells This study BioProject: PRJNA1344834 H3K27ac AQuA-HiChIP of HAP1 cells This study BioProject: PRJNA1344834 Experimental models: Cell lines HAP1 Guo et al.24 N/A HEK293FT Thermo Cat# R70007 K562 ATCC Cat# CCL-243 MDA-MB-231 ATCC Cat# HTB-26 THP1 Wessels and Méndez-Mancilla et al.48 N/A HAP1 RfxCas13d Guo et al.24 N/A HEK293FT RfxCas13d Wessels and Méndez-Mancilla et al.23 N/A (Continued on next page) Cell Genomics 6, 101253, July 8, 2026 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER K562 RfxCas13d This study N/A MDA-MB-231 RfxCas13d This study N/A THP1 RfxCas13d Wessels and Méndez-Mancilla et al.48 N/A Oligonucleotides Guide RNA sequences, see Tables S1B, S3A, and S4A This study N/A lncRNA-targeting siRNA sequences, see Table S3D This study N/A RT-qPCR oligo sequences, see Table S3B This study N/A Recombinant DNA pLentiRNACRISPR_007 - TetO-NLSRfxCas13d- NLS-WPRE-EFS-rtTA3-2ABlast Wessels and Méndez-Mancilla et al.23 Addgene 138149 pLentiRNAGuide_001 - hU6-RfxCas13dDR1- BsmBI-EFS-Puro-WPRE Wessels and Méndez-Mancilla et al.23 Addgene 138150 pLentiRNAGuide_004 - hU6-RfxCas13dDR1- EGFP-P2A-PuroR Hart et al.34 Addgene 223175 tFUCCI(CA)5 Ando et al.43 Addgene 153521 pLentiFUCCI(CA)5 This study Addgene 223176 pMD2.G Didier Trono Addgene 12259 psPAX2 Didier Trono Addgene 12260 Software and algorithms Cas13 design tool Guo et al.24 https://cas13design.nygenome.org/ Cas13 guide design algorithm Wessels and Méndez-Mancilla et al.23 https://gitlab.com/sanjanalab/cas13 TIGER gRNA design Wessels and Stirn et al.78 https://tiger.nygenome.org/ Cutadapt v.1.13 Martin79 https://cutadapt.readthedocs.io/en/stable/ Bowtie v.1.1.2 Langmead et al.80 https://bowtie-bio.sourceforge.net/index. shtml SVA v.3.34.0 Leek et al.81 https://bioconductor.org/packages/ release/bioc/html/sva.html RobustRankAggreg v1.2.1 Kolde et al.82 https://cran.r-project.org/web/packages/ RobustRankAggreg/index.html STAR Dobin et al.83 https://github.com/alexdobin/STAR RSEM Li and Dewey84 https://github.com/deweylab/RSEM Tximport Soneson et al.85 https://bioconductor.org/packages/ release/bioc/html/tximport.html DESeq2 v.3.19 Love et al.86 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html survival v.3.2.7 Therneau et al.87,88 https://CRAN.R-project.org/ package=survival survminer v.0.4.9 Kassambara et al.89 https://rpkgs.datanovia.com/survminer/ index.html clusterProfiler v4.10.0 Yu et al.90 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html MSigDB v2023.2 Subramanian et al. https://www.gsea-msigdb.org/gsea/ msigdb/collections.jsp 10x Genomics Cell Ranger v9.0.0 Zheng et al.91 https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat v4.1.1 Hao et al.92 https://satijalab.org/seurat/ FeatureCounts v2.0.4 Liao et al.93 https://subread.sourceforge.net/ featureCounts.html (Continued on next page) e3 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS

    Staining:

    Article Title: Essential lncRNAs in the human transcriptome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-HA peptide antibody Cell Signaling Technology Cat# 2367S; RRID: AB_10691311 Anti-H3k27ac antibody Active Motif Cat# 39133; RRID: AB_2561016 Bacterial and virus strains NEB Stable Cells New England Biolabs Cat# C3040I Endura Electrocompetent Cells Lucigen Cat# 60242–2 Chemicals, peptides, and recombinant proteins Polyethyleneimine Polysciences Cat# 23966 Puromycin Invivogen Cat# ant-pr-1 Blasticidin S A.G. Scientific Cat# B-1247-SOL Doxycycline Sigma-Aldrich Cat# D3447 Doxorubicin MedChemExpress Cat# HY-15142 Dinaciclib MedChemExpress Cat# HY-10492 Critical commercial assays KAPA Total RNA-seq kit with RiboErase Roche Cat# 07962282001 Stranded mRNA Prep Illumina Cat# 20040532 RNA UD Indexes, Set A Illumina Cat# 20040553 Chromium Single Cell 3′ Gene Expression v3.1 with feature barcoding technology for CRISPR screening 10x Genomics Cat# 10000127, 10000268 and 10000262 TaqB polymerase Enzymatics Cat# P7250L 2× Rapid Ligase Buffer Enzymatics Cat# B1010L Q5 High-Fidelity DNA Polymerase NEB Cat# M0491 T7 DNA Ligase NEB Cat# M0318L T4 DNA Ligase NEB Cat# B0202S Gibson Assembly Master Mix NEB Cat# E2611L KAPA HiFi HotStart ReadyMix PCR Kit Roche Cat# 07958935001 SPRI beads Beckman Cat# B23317 MAXI Fast-Ion Plasmid Purification Kit IBI Scientific Cat# IB47125 QIAGEN Plasmid Mini Kit Qiagen Cat# 12123 QiaQuick Gel Extraction Kit Qiagen Cat# 28704 DNA Clean & Concentrator Zymo Cat# D4014 Qubit RNA XR Assay Kit Thermo Cat# Q10210 Qubit dsDNA HS Assay Kit Thermo Cat# Q32851 FastDigest Esp3I Thermo Cat# FD0454 FastDigest LguI Thermo Cat# FD1934 FastDigest NheI Thermo Cat# FD0974 FastDigest ApaI Thermo Cat# FD1414 FastDigest BamHI Thermo Cat# FD0055 FastDigest KpnI Thermo Cat# FD0524 FastAP Thermosensitive Alkaline Phosphatase Thermo Cat# EF0651 Qubit RNA XR Assay Kit Thermo Cat# Q10210 MboI NEB Cat# R0147M DNA Polymerase I Large (Klenow) Fragment NEB Cat# M0210L (Continued on next page) e1 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-14-dATP Thermo Cat# 19524016 Direct-zol RNA Purification Kit Zymo Cat# R2062 Agilent High Sensitivity DNA Kit Agilent Cat# 5067–4626 RevertAid Reverse Transcriptase Thermo Cat# EP0442 Luna Universal qPCR Master Mix NEB Cat# M3003E Lipofectamine RNAiMAX Thermo Cat# 13778075 LIVE/DEAD Fixable Violet Dead Cell Stain Kit Thermo Cat# L34963 Incucyte Annexin V Dye for Apoptosis Sartorius Cat# 4642 Proteinase K NEB Cat# P8107S RNase A A.G.Scientific Cat# R-2000 TE Buffer Sigma Cat# 93283 Dynabeads Protein A Thermo Cat# 10001D Dynabeads M-280 Streptavidin Thermo Cat# 11205D Deposited data MDA-MB-231 total RNA-seq fastq RNA atlas76 N/A Developmental lncRNA annotation (human.lncRNA.gtf) Sarropoulos et al.19 N/A Developmental samples Sarropoulos et al.19 and Cardoso-Moreira et al.52 N/A Fastq files of TCGA RNA-seq samples TCGA, dbGaP (phs000178.v11.p8) https://portal.gdc.cancer.gov/, https:// www.ncbi.nlm.nih.gov/projects/gap/cgibin/study.cgi?study_id=phs000178.v11.p8 GRCh38 reference genome (GRCh38.d1.vd1.fa.tar) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files GENCODE v36 (gencode.v36.annotation.gtf.gz) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files 10x Genomics reference (refdata-gexGRCh38-2024-A) 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads HISAT2 indexes (UCSC hg38) HISAT2 https://daehwankimlab.github.io/hisat2/ download/ K562 and KBM7 Hi-C TADs bed files (TADs in hg38) Hi-C genome Browser77 http://3dgenome.fsm.northwestern.edu/ publications.html) Pooled transcriptome-scale RNA-targeting Cas13 screens This study BioProject: PRJNA1344834 Total RNA-seq of parental and Cas13engineered cells This study BioProject: PRJNA1344834 Stranded RNA-seq with polyA-enrichment of Cas13-engineered cells This study BioProject: PRJNA1344834 CaRPool-seq of MDA-MB-231 and HAP1 perturbed cells This study BioProject: PRJNA1344834 mRNA-seq of MDA-MB-231 perturbed cells This study BioProject: PRJNA1344834 H3K27ac AQuA-HiChIP of HAP1 cells This study BioProject: PRJNA1344834 Experimental models: Cell lines HAP1 Guo et al.24 N/A HEK293FT Thermo Cat# R70007 K562 ATCC Cat# CCL-243 MDA-MB-231 ATCC Cat# HTB-26 THP1 Wessels and Méndez-Mancilla et al.48 N/A HAP1 RfxCas13d Guo et al.24 N/A HEK293FT RfxCas13d Wessels and Méndez-Mancilla et al.23 N/A (Continued on next page) Cell Genomics 6, 101253, July 8, 2026 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER K562 RfxCas13d This study N/A MDA-MB-231 RfxCas13d This study N/A THP1 RfxCas13d Wessels and Méndez-Mancilla et al.48 N/A Oligonucleotides Guide RNA sequences, see Tables S1B, S3A, and S4A This study N/A lncRNA-targeting siRNA sequences, see Table S3D This study N/A RT-qPCR oligo sequences, see Table S3B This study N/A Recombinant DNA pLentiRNACRISPR_007 - TetO-NLSRfxCas13d- NLS-WPRE-EFS-rtTA3-2ABlast Wessels and Méndez-Mancilla et al.23 Addgene 138149 pLentiRNAGuide_001 - hU6-RfxCas13dDR1- BsmBI-EFS-Puro-WPRE Wessels and Méndez-Mancilla et al.23 Addgene 138150 pLentiRNAGuide_004 - hU6-RfxCas13dDR1- EGFP-P2A-PuroR Hart et al.34 Addgene 223175 tFUCCI(CA)5 Ando et al.43 Addgene 153521 pLentiFUCCI(CA)5 This study Addgene 223176 pMD2.G Didier Trono Addgene 12259 psPAX2 Didier Trono Addgene 12260 Software and algorithms Cas13 design tool Guo et al.24 https://cas13design.nygenome.org/ Cas13 guide design algorithm Wessels and Méndez-Mancilla et al.23 https://gitlab.com/sanjanalab/cas13 TIGER gRNA design Wessels and Stirn et al.78 https://tiger.nygenome.org/ Cutadapt v.1.13 Martin79 https://cutadapt.readthedocs.io/en/stable/ Bowtie v.1.1.2 Langmead et al.80 https://bowtie-bio.sourceforge.net/index. shtml SVA v.3.34.0 Leek et al.81 https://bioconductor.org/packages/ release/bioc/html/sva.html RobustRankAggreg v1.2.1 Kolde et al.82 https://cran.r-project.org/web/packages/ RobustRankAggreg/index.html STAR Dobin et al.83 https://github.com/alexdobin/STAR RSEM Li and Dewey84 https://github.com/deweylab/RSEM Tximport Soneson et al.85 https://bioconductor.org/packages/ release/bioc/html/tximport.html DESeq2 v.3.19 Love et al.86 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html survival v.3.2.7 Therneau et al.87,88 https://CRAN.R-project.org/ package=survival survminer v.0.4.9 Kassambara et al.89 https://rpkgs.datanovia.com/survminer/ index.html clusterProfiler v4.10.0 Yu et al.90 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html MSigDB v2023.2 Subramanian et al. https://www.gsea-msigdb.org/gsea/ msigdb/collections.jsp 10x Genomics Cell Ranger v9.0.0 Zheng et al.91 https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat v4.1.1 Hao et al.92 https://satijalab.org/seurat/ FeatureCounts v2.0.4 Liao et al.93 https://subread.sourceforge.net/ featureCounts.html (Continued on next page) e3 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS

    RNA Sequencing:

    Article Title: Essential lncRNAs in the human transcriptome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-HA peptide antibody Cell Signaling Technology Cat# 2367S; RRID: AB_10691311 Anti-H3k27ac antibody Active Motif Cat# 39133; RRID: AB_2561016 Bacterial and virus strains NEB Stable Cells New England Biolabs Cat# C3040I Endura Electrocompetent Cells Lucigen Cat# 60242–2 Chemicals, peptides, and recombinant proteins Polyethyleneimine Polysciences Cat# 23966 Puromycin Invivogen Cat# ant-pr-1 Blasticidin S A.G. Scientific Cat# B-1247-SOL Doxycycline Sigma-Aldrich Cat# D3447 Doxorubicin MedChemExpress Cat# HY-15142 Dinaciclib MedChemExpress Cat# HY-10492 Critical commercial assays KAPA Total RNA-seq kit with RiboErase Roche Cat# 07962282001 Stranded mRNA Prep Illumina Cat# 20040532 RNA UD Indexes, Set A Illumina Cat# 20040553 Chromium Single Cell 3′ Gene Expression v3.1 with feature barcoding technology for CRISPR screening 10x Genomics Cat# 10000127, 10000268 and 10000262 TaqB polymerase Enzymatics Cat# P7250L 2× Rapid Ligase Buffer Enzymatics Cat# B1010L Q5 High-Fidelity DNA Polymerase NEB Cat# M0491 T7 DNA Ligase NEB Cat# M0318L T4 DNA Ligase NEB Cat# B0202S Gibson Assembly Master Mix NEB Cat# E2611L KAPA HiFi HotStart ReadyMix PCR Kit Roche Cat# 07958935001 SPRI beads Beckman Cat# B23317 MAXI Fast-Ion Plasmid Purification Kit IBI Scientific Cat# IB47125 QIAGEN Plasmid Mini Kit Qiagen Cat# 12123 QiaQuick Gel Extraction Kit Qiagen Cat# 28704 DNA Clean & Concentrator Zymo Cat# D4014 Qubit RNA XR Assay Kit Thermo Cat# Q10210 Qubit dsDNA HS Assay Kit Thermo Cat# Q32851 FastDigest Esp3I Thermo Cat# FD0454 FastDigest LguI Thermo Cat# FD1934 FastDigest NheI Thermo Cat# FD0974 FastDigest ApaI Thermo Cat# FD1414 FastDigest BamHI Thermo Cat# FD0055 FastDigest KpnI Thermo Cat# FD0524 FastAP Thermosensitive Alkaline Phosphatase Thermo Cat# EF0651 Qubit RNA XR Assay Kit Thermo Cat# Q10210 MboI NEB Cat# R0147M DNA Polymerase I Large (Klenow) Fragment NEB Cat# M0210L (Continued on next page) e1 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-14-dATP Thermo Cat# 19524016 Direct-zol RNA Purification Kit Zymo Cat# R2062 Agilent High Sensitivity DNA Kit Agilent Cat# 5067–4626 RevertAid Reverse Transcriptase Thermo Cat# EP0442 Luna Universal qPCR Master Mix NEB Cat# M3003E Lipofectamine RNAiMAX Thermo Cat# 13778075 LIVE/DEAD Fixable Violet Dead Cell Stain Kit Thermo Cat# L34963 Incucyte Annexin V Dye for Apoptosis Sartorius Cat# 4642 Proteinase K NEB Cat# P8107S RNase A A.G.Scientific Cat# R-2000 TE Buffer Sigma Cat# 93283 Dynabeads Protein A Thermo Cat# 10001D Dynabeads M-280 Streptavidin Thermo Cat# 11205D Deposited data MDA-MB-231 total RNA-seq fastq RNA atlas76 N/A Developmental lncRNA annotation (human.lncRNA.gtf) Sarropoulos et al.19 N/A Developmental samples Sarropoulos et al.19 and Cardoso-Moreira et al.52 N/A Fastq files of TCGA RNA-seq samples TCGA, dbGaP (phs000178.v11.p8) https://portal.gdc.cancer.gov/, https:// www.ncbi.nlm.nih.gov/projects/gap/cgibin/study.cgi?study_id=phs000178.v11.p8 GRCh38 reference genome (GRCh38.d1.vd1.fa.tar) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files GENCODE v36 (gencode.v36.annotation.gtf.gz) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files 10x Genomics reference (refdata-gexGRCh38-2024-A) 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads HISAT2 indexes (UCSC hg38) HISAT2 https://daehwankimlab.github.io/hisat2/ download/ K562 and KBM7 Hi-C TADs bed files (TADs in hg38) Hi-C genome Browser77 http://3dgenome.fsm.northwestern.edu/ publications.html) Pooled transcriptome-scale RNA-targeting Cas13 screens This study BioProject: PRJNA1344834 Total RNA-seq of parental and Cas13engineered cells This study BioProject: PRJNA1344834 Stranded RNA-seq with polyA-enrichment of Cas13-engineered cells This study BioProject: PRJNA1344834 CaRPool-seq of MDA-MB-231 and HAP1 perturbed cells This study BioProject: PRJNA1344834 mRNA-seq of MDA-MB-231 perturbed cells This study BioProject: PRJNA1344834 H3K27ac AQuA-HiChIP of HAP1 cells This study BioProject: PRJNA1344834 Experimental models: Cell lines HAP1 Guo et al.24 N/A HEK293FT Thermo Cat# R70007 K562 ATCC Cat# CCL-243 MDA-MB-231 ATCC Cat# HTB-26 THP1 Wessels and Méndez-Mancilla et al.48 N/A HAP1 RfxCas13d Guo et al.24 N/A HEK293FT RfxCas13d Wessels and Méndez-Mancilla et al.23 N/A (Continued on next page) Cell Genomics 6, 101253, July 8, 2026 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER K562 RfxCas13d This study N/A MDA-MB-231 RfxCas13d This study N/A THP1 RfxCas13d Wessels and Méndez-Mancilla et al.48 N/A Oligonucleotides Guide RNA sequences, see Tables S1B, S3A, and S4A This study N/A lncRNA-targeting siRNA sequences, see Table S3D This study N/A RT-qPCR oligo sequences, see Table S3B This study N/A Recombinant DNA pLentiRNACRISPR_007 - TetO-NLSRfxCas13d- NLS-WPRE-EFS-rtTA3-2ABlast Wessels and Méndez-Mancilla et al.23 Addgene 138149 pLentiRNAGuide_001 - hU6-RfxCas13dDR1- BsmBI-EFS-Puro-WPRE Wessels and Méndez-Mancilla et al.23 Addgene 138150 pLentiRNAGuide_004 - hU6-RfxCas13dDR1- EGFP-P2A-PuroR Hart et al.34 Addgene 223175 tFUCCI(CA)5 Ando et al.43 Addgene 153521 pLentiFUCCI(CA)5 This study Addgene 223176 pMD2.G Didier Trono Addgene 12259 psPAX2 Didier Trono Addgene 12260 Software and algorithms Cas13 design tool Guo et al.24 https://cas13design.nygenome.org/ Cas13 guide design algorithm Wessels and Méndez-Mancilla et al.23 https://gitlab.com/sanjanalab/cas13 TIGER gRNA design Wessels and Stirn et al.78 https://tiger.nygenome.org/ Cutadapt v.1.13 Martin79 https://cutadapt.readthedocs.io/en/stable/ Bowtie v.1.1.2 Langmead et al.80 https://bowtie-bio.sourceforge.net/index. shtml SVA v.3.34.0 Leek et al.81 https://bioconductor.org/packages/ release/bioc/html/sva.html RobustRankAggreg v1.2.1 Kolde et al.82 https://cran.r-project.org/web/packages/ RobustRankAggreg/index.html STAR Dobin et al.83 https://github.com/alexdobin/STAR RSEM Li and Dewey84 https://github.com/deweylab/RSEM Tximport Soneson et al.85 https://bioconductor.org/packages/ release/bioc/html/tximport.html DESeq2 v.3.19 Love et al.86 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html survival v.3.2.7 Therneau et al.87,88 https://CRAN.R-project.org/ package=survival survminer v.0.4.9 Kassambara et al.89 https://rpkgs.datanovia.com/survminer/ index.html clusterProfiler v4.10.0 Yu et al.90 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html MSigDB v2023.2 Subramanian et al. https://www.gsea-msigdb.org/gsea/ msigdb/collections.jsp 10x Genomics Cell Ranger v9.0.0 Zheng et al.91 https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat v4.1.1 Hao et al.92 https://satijalab.org/seurat/ FeatureCounts v2.0.4 Liao et al.93 https://subread.sourceforge.net/ featureCounts.html (Continued on next page) e3 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS

    Software:

    Article Title: Essential lncRNAs in the human transcriptome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-HA peptide antibody Cell Signaling Technology Cat# 2367S; RRID: AB_10691311 Anti-H3k27ac antibody Active Motif Cat# 39133; RRID: AB_2561016 Bacterial and virus strains NEB Stable Cells New England Biolabs Cat# C3040I Endura Electrocompetent Cells Lucigen Cat# 60242–2 Chemicals, peptides, and recombinant proteins Polyethyleneimine Polysciences Cat# 23966 Puromycin Invivogen Cat# ant-pr-1 Blasticidin S A.G. Scientific Cat# B-1247-SOL Doxycycline Sigma-Aldrich Cat# D3447 Doxorubicin MedChemExpress Cat# HY-15142 Dinaciclib MedChemExpress Cat# HY-10492 Critical commercial assays KAPA Total RNA-seq kit with RiboErase Roche Cat# 07962282001 Stranded mRNA Prep Illumina Cat# 20040532 RNA UD Indexes, Set A Illumina Cat# 20040553 Chromium Single Cell 3′ Gene Expression v3.1 with feature barcoding technology for CRISPR screening 10x Genomics Cat# 10000127, 10000268 and 10000262 TaqB polymerase Enzymatics Cat# P7250L 2× Rapid Ligase Buffer Enzymatics Cat# B1010L Q5 High-Fidelity DNA Polymerase NEB Cat# M0491 T7 DNA Ligase NEB Cat# M0318L T4 DNA Ligase NEB Cat# B0202S Gibson Assembly Master Mix NEB Cat# E2611L KAPA HiFi HotStart ReadyMix PCR Kit Roche Cat# 07958935001 SPRI beads Beckman Cat# B23317 MAXI Fast-Ion Plasmid Purification Kit IBI Scientific Cat# IB47125 QIAGEN Plasmid Mini Kit Qiagen Cat# 12123 QiaQuick Gel Extraction Kit Qiagen Cat# 28704 DNA Clean & Concentrator Zymo Cat# D4014 Qubit RNA XR Assay Kit Thermo Cat# Q10210 Qubit dsDNA HS Assay Kit Thermo Cat# Q32851 FastDigest Esp3I Thermo Cat# FD0454 FastDigest LguI Thermo Cat# FD1934 FastDigest NheI Thermo Cat# FD0974 FastDigest ApaI Thermo Cat# FD1414 FastDigest BamHI Thermo Cat# FD0055 FastDigest KpnI Thermo Cat# FD0524 FastAP Thermosensitive Alkaline Phosphatase Thermo Cat# EF0651 Qubit RNA XR Assay Kit Thermo Cat# Q10210 MboI NEB Cat# R0147M DNA Polymerase I Large (Klenow) Fragment NEB Cat# M0210L (Continued on next page) e1 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-14-dATP Thermo Cat# 19524016 Direct-zol RNA Purification Kit Zymo Cat# R2062 Agilent High Sensitivity DNA Kit Agilent Cat# 5067–4626 RevertAid Reverse Transcriptase Thermo Cat# EP0442 Luna Universal qPCR Master Mix NEB Cat# M3003E Lipofectamine RNAiMAX Thermo Cat# 13778075 LIVE/DEAD Fixable Violet Dead Cell Stain Kit Thermo Cat# L34963 Incucyte Annexin V Dye for Apoptosis Sartorius Cat# 4642 Proteinase K NEB Cat# P8107S RNase A A.G.Scientific Cat# R-2000 TE Buffer Sigma Cat# 93283 Dynabeads Protein A Thermo Cat# 10001D Dynabeads M-280 Streptavidin Thermo Cat# 11205D Deposited data MDA-MB-231 total RNA-seq fastq RNA atlas76 N/A Developmental lncRNA annotation (human.lncRNA.gtf) Sarropoulos et al.19 N/A Developmental samples Sarropoulos et al.19 and Cardoso-Moreira et al.52 N/A Fastq files of TCGA RNA-seq samples TCGA, dbGaP (phs000178.v11.p8) https://portal.gdc.cancer.gov/, https:// www.ncbi.nlm.nih.gov/projects/gap/cgibin/study.cgi?study_id=phs000178.v11.p8 GRCh38 reference genome (GRCh38.d1.vd1.fa.tar) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files GENCODE v36 (gencode.v36.annotation.gtf.gz) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files 10x Genomics reference (refdata-gexGRCh38-2024-A) 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads HISAT2 indexes (UCSC hg38) HISAT2 https://daehwankimlab.github.io/hisat2/ download/ K562 and KBM7 Hi-C TADs bed files (TADs in hg38) Hi-C genome Browser77 http://3dgenome.fsm.northwestern.edu/ publications.html) Pooled transcriptome-scale RNA-targeting Cas13 screens This study BioProject: PRJNA1344834 Total RNA-seq of parental and Cas13engineered cells This study BioProject: PRJNA1344834 Stranded RNA-seq with polyA-enrichment of Cas13-engineered cells This study BioProject: PRJNA1344834 CaRPool-seq of MDA-MB-231 and HAP1 perturbed cells This study BioProject: PRJNA1344834 mRNA-seq of MDA-MB-231 perturbed cells This study BioProject: PRJNA1344834 H3K27ac AQuA-HiChIP of HAP1 cells This study BioProject: PRJNA1344834 Experimental models: Cell lines HAP1 Guo et al.24 N/A HEK293FT Thermo Cat# R70007 K562 ATCC Cat# CCL-243 MDA-MB-231 ATCC Cat# HTB-26 THP1 Wessels and Méndez-Mancilla et al.48 N/A HAP1 RfxCas13d Guo et al.24 N/A HEK293FT RfxCas13d Wessels and Méndez-Mancilla et al.23 N/A (Continued on next page) Cell Genomics 6, 101253, July 8, 2026 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER K562 RfxCas13d This study N/A MDA-MB-231 RfxCas13d This study N/A THP1 RfxCas13d Wessels and Méndez-Mancilla et al.48 N/A Oligonucleotides Guide RNA sequences, see Tables S1B, S3A, and S4A This study N/A lncRNA-targeting siRNA sequences, see Table S3D This study N/A RT-qPCR oligo sequences, see Table S3B This study N/A Recombinant DNA pLentiRNACRISPR_007 - TetO-NLSRfxCas13d- NLS-WPRE-EFS-rtTA3-2ABlast Wessels and Méndez-Mancilla et al.23 Addgene 138149 pLentiRNAGuide_001 - hU6-RfxCas13dDR1- BsmBI-EFS-Puro-WPRE Wessels and Méndez-Mancilla et al.23 Addgene 138150 pLentiRNAGuide_004 - hU6-RfxCas13dDR1- EGFP-P2A-PuroR Hart et al.34 Addgene 223175 tFUCCI(CA)5 Ando et al.43 Addgene 153521 pLentiFUCCI(CA)5 This study Addgene 223176 pMD2.G Didier Trono Addgene 12259 psPAX2 Didier Trono Addgene 12260 Software and algorithms Cas13 design tool Guo et al.24 https://cas13design.nygenome.org/ Cas13 guide design algorithm Wessels and Méndez-Mancilla et al.23 https://gitlab.com/sanjanalab/cas13 TIGER gRNA design Wessels and Stirn et al.78 https://tiger.nygenome.org/ Cutadapt v.1.13 Martin79 https://cutadapt.readthedocs.io/en/stable/ Bowtie v.1.1.2 Langmead et al.80 https://bowtie-bio.sourceforge.net/index. shtml SVA v.3.34.0 Leek et al.81 https://bioconductor.org/packages/ release/bioc/html/sva.html RobustRankAggreg v1.2.1 Kolde et al.82 https://cran.r-project.org/web/packages/ RobustRankAggreg/index.html STAR Dobin et al.83 https://github.com/alexdobin/STAR RSEM Li and Dewey84 https://github.com/deweylab/RSEM Tximport Soneson et al.85 https://bioconductor.org/packages/ release/bioc/html/tximport.html DESeq2 v.3.19 Love et al.86 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html survival v.3.2.7 Therneau et al.87,88 https://CRAN.R-project.org/ package=survival survminer v.0.4.9 Kassambara et al.89 https://rpkgs.datanovia.com/survminer/ index.html clusterProfiler v4.10.0 Yu et al.90 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html MSigDB v2023.2 Subramanian et al. https://www.gsea-msigdb.org/gsea/ msigdb/collections.jsp 10x Genomics Cell Ranger v9.0.0 Zheng et al.91 https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat v4.1.1 Hao et al.92 https://satijalab.org/seurat/ FeatureCounts v2.0.4 Liao et al.93 https://subread.sourceforge.net/ featureCounts.html (Continued on next page) e3 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS

    Hi-C:

    Article Title: Essential lncRNAs in the human transcriptome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-HA peptide antibody Cell Signaling Technology Cat# 2367S; RRID: AB_10691311 Anti-H3k27ac antibody Active Motif Cat# 39133; RRID: AB_2561016 Bacterial and virus strains NEB Stable Cells New England Biolabs Cat# C3040I Endura Electrocompetent Cells Lucigen Cat# 60242–2 Chemicals, peptides, and recombinant proteins Polyethyleneimine Polysciences Cat# 23966 Puromycin Invivogen Cat# ant-pr-1 Blasticidin S A.G. Scientific Cat# B-1247-SOL Doxycycline Sigma-Aldrich Cat# D3447 Doxorubicin MedChemExpress Cat# HY-15142 Dinaciclib MedChemExpress Cat# HY-10492 Critical commercial assays KAPA Total RNA-seq kit with RiboErase Roche Cat# 07962282001 Stranded mRNA Prep Illumina Cat# 20040532 RNA UD Indexes, Set A Illumina Cat# 20040553 Chromium Single Cell 3′ Gene Expression v3.1 with feature barcoding technology for CRISPR screening 10x Genomics Cat# 10000127, 10000268 and 10000262 TaqB polymerase Enzymatics Cat# P7250L 2× Rapid Ligase Buffer Enzymatics Cat# B1010L Q5 High-Fidelity DNA Polymerase NEB Cat# M0491 T7 DNA Ligase NEB Cat# M0318L T4 DNA Ligase NEB Cat# B0202S Gibson Assembly Master Mix NEB Cat# E2611L KAPA HiFi HotStart ReadyMix PCR Kit Roche Cat# 07958935001 SPRI beads Beckman Cat# B23317 MAXI Fast-Ion Plasmid Purification Kit IBI Scientific Cat# IB47125 QIAGEN Plasmid Mini Kit Qiagen Cat# 12123 QiaQuick Gel Extraction Kit Qiagen Cat# 28704 DNA Clean & Concentrator Zymo Cat# D4014 Qubit RNA XR Assay Kit Thermo Cat# Q10210 Qubit dsDNA HS Assay Kit Thermo Cat# Q32851 FastDigest Esp3I Thermo Cat# FD0454 FastDigest LguI Thermo Cat# FD1934 FastDigest NheI Thermo Cat# FD0974 FastDigest ApaI Thermo Cat# FD1414 FastDigest BamHI Thermo Cat# FD0055 FastDigest KpnI Thermo Cat# FD0524 FastAP Thermosensitive Alkaline Phosphatase Thermo Cat# EF0651 Qubit RNA XR Assay Kit Thermo Cat# Q10210 MboI NEB Cat# R0147M DNA Polymerase I Large (Klenow) Fragment NEB Cat# M0210L (Continued on next page) e1 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin-14-dATP Thermo Cat# 19524016 Direct-zol RNA Purification Kit Zymo Cat# R2062 Agilent High Sensitivity DNA Kit Agilent Cat# 5067–4626 RevertAid Reverse Transcriptase Thermo Cat# EP0442 Luna Universal qPCR Master Mix NEB Cat# M3003E Lipofectamine RNAiMAX Thermo Cat# 13778075 LIVE/DEAD Fixable Violet Dead Cell Stain Kit Thermo Cat# L34963 Incucyte Annexin V Dye for Apoptosis Sartorius Cat# 4642 Proteinase K NEB Cat# P8107S RNase A A.G.Scientific Cat# R-2000 TE Buffer Sigma Cat# 93283 Dynabeads Protein A Thermo Cat# 10001D Dynabeads M-280 Streptavidin Thermo Cat# 11205D Deposited data MDA-MB-231 total RNA-seq fastq RNA atlas76 N/A Developmental lncRNA annotation (human.lncRNA.gtf) Sarropoulos et al.19 N/A Developmental samples Sarropoulos et al.19 and Cardoso-Moreira et al.52 N/A Fastq files of TCGA RNA-seq samples TCGA, dbGaP (phs000178.v11.p8) https://portal.gdc.cancer.gov/, https:// www.ncbi.nlm.nih.gov/projects/gap/cgibin/study.cgi?study_id=phs000178.v11.p8 GRCh38 reference genome (GRCh38.d1.vd1.fa.tar) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files GENCODE v36 (gencode.v36.annotation.gtf.gz) GENCODE https://gdc.cancer.gov/about-data/gdc- data-processing/gdc-reference-files 10x Genomics reference (refdata-gexGRCh38-2024-A) 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads HISAT2 indexes (UCSC hg38) HISAT2 https://daehwankimlab.github.io/hisat2/ download/ K562 and KBM7 Hi-C TADs bed files (TADs in hg38) Hi-C genome Browser77 http://3dgenome.fsm.northwestern.edu/ publications.html) Pooled transcriptome-scale RNA-targeting Cas13 screens This study BioProject: PRJNA1344834 Total RNA-seq of parental and Cas13engineered cells This study BioProject: PRJNA1344834 Stranded RNA-seq with polyA-enrichment of Cas13-engineered cells This study BioProject: PRJNA1344834 CaRPool-seq of MDA-MB-231 and HAP1 perturbed cells This study BioProject: PRJNA1344834 mRNA-seq of MDA-MB-231 perturbed cells This study BioProject: PRJNA1344834 H3K27ac AQuA-HiChIP of HAP1 cells This study BioProject: PRJNA1344834 Experimental models: Cell lines HAP1 Guo et al.24 N/A HEK293FT Thermo Cat# R70007 K562 ATCC Cat# CCL-243 MDA-MB-231 ATCC Cat# HTB-26 THP1 Wessels and Méndez-Mancilla et al.48 N/A HAP1 RfxCas13d Guo et al.24 N/A HEK293FT RfxCas13d Wessels and Méndez-Mancilla et al.23 N/A (Continued on next page) Cell Genomics 6, 101253, July 8, 2026 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER K562 RfxCas13d This study N/A MDA-MB-231 RfxCas13d This study N/A THP1 RfxCas13d Wessels and Méndez-Mancilla et al.48 N/A Oligonucleotides Guide RNA sequences, see Tables S1B, S3A, and S4A This study N/A lncRNA-targeting siRNA sequences, see Table S3D This study N/A RT-qPCR oligo sequences, see Table S3B This study N/A Recombinant DNA pLentiRNACRISPR_007 - TetO-NLSRfxCas13d- NLS-WPRE-EFS-rtTA3-2ABlast Wessels and Méndez-Mancilla et al.23 Addgene 138149 pLentiRNAGuide_001 - hU6-RfxCas13dDR1- BsmBI-EFS-Puro-WPRE Wessels and Méndez-Mancilla et al.23 Addgene 138150 pLentiRNAGuide_004 - hU6-RfxCas13dDR1- EGFP-P2A-PuroR Hart et al.34 Addgene 223175 tFUCCI(CA)5 Ando et al.43 Addgene 153521 pLentiFUCCI(CA)5 This study Addgene 223176 pMD2.G Didier Trono Addgene 12259 psPAX2 Didier Trono Addgene 12260 Software and algorithms Cas13 design tool Guo et al.24 https://cas13design.nygenome.org/ Cas13 guide design algorithm Wessels and Méndez-Mancilla et al.23 https://gitlab.com/sanjanalab/cas13 TIGER gRNA design Wessels and Stirn et al.78 https://tiger.nygenome.org/ Cutadapt v.1.13 Martin79 https://cutadapt.readthedocs.io/en/stable/ Bowtie v.1.1.2 Langmead et al.80 https://bowtie-bio.sourceforge.net/index. shtml SVA v.3.34.0 Leek et al.81 https://bioconductor.org/packages/ release/bioc/html/sva.html RobustRankAggreg v1.2.1 Kolde et al.82 https://cran.r-project.org/web/packages/ RobustRankAggreg/index.html STAR Dobin et al.83 https://github.com/alexdobin/STAR RSEM Li and Dewey84 https://github.com/deweylab/RSEM Tximport Soneson et al.85 https://bioconductor.org/packages/ release/bioc/html/tximport.html DESeq2 v.3.19 Love et al.86 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html survival v.3.2.7 Therneau et al.87,88 https://CRAN.R-project.org/ package=survival survminer v.0.4.9 Kassambara et al.89 https://rpkgs.datanovia.com/survminer/ index.html clusterProfiler v4.10.0 Yu et al.90 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html MSigDB v2023.2 Subramanian et al. https://www.gsea-msigdb.org/gsea/ msigdb/collections.jsp 10x Genomics Cell Ranger v9.0.0 Zheng et al.91 https://www.10xgenomics.com/support/ software/cell-ranger/latest Seurat v4.1.1 Hao et al.92 https://satijalab.org/seurat/ FeatureCounts v2.0.4 Liao et al.93 https://subread.sourceforge.net/ featureCounts.html (Continued on next page) e3 Cell Genomics 6, 101253, July 8, 2026 Article ll OPEN ACCESS



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    CEP exerts cytotoxicity in TNBC cells. (A) Chemical structure of CEP. (B) CEP inhibited TNBC cell viability. The effect of CEP treatment on TNBC cell viability after 24, 48 and 72 h. (C) CEP inhibited clonogenicity of MDA-MB-231 and Hs578T cells. n=3; *P < 0.05, **P < 0.01 and ***P < 0.001 vs. control. CEP, cepharanthine; TNBC, triple-negative breast cancer.

    Journal: Molecular Medicine Reports

    Article Title: Cepharanthine inhibits lysosomes and induces apoptosis in triple-negative breast cancer cells

    doi: 10.3892/mmr.2026.13899

    Figure Lengend Snippet: CEP exerts cytotoxicity in TNBC cells. (A) Chemical structure of CEP. (B) CEP inhibited TNBC cell viability. The effect of CEP treatment on TNBC cell viability after 24, 48 and 72 h. (C) CEP inhibited clonogenicity of MDA-MB-231 and Hs578T cells. n=3; *P < 0.05, **P < 0.01 and ***P < 0.001 vs. control. CEP, cepharanthine; TNBC, triple-negative breast cancer.

    Article Snippet: The TNBC cell lines MDA-MB-231 (cat. no. CL-0150; Procell Life Science & Technology Co., Ltd.) and Hs578T (cat. no. CL-0114; Procell Life Science & Technology Co., Ltd.) were cultured in high-glucose DMEM medium (cat. no. C11965500BT; Gibco; Thermo Fisher Scientific, Inc.), supplemented with 10% fetal bovine serum (cat. no. 164210; Procell Life Science & Technology Co., Ltd.) and 1% penicillin/streptomycin (cat. no. 15140122; Gibco; Thermo Fisher Scientific, Inc.).

    Techniques: Control

    CEP induces apoptosis in triple-negative breast cancer cells. Flow cytometric quantification of apoptosis induced by CEP in (A) MDA-MB-231 and (B) Hs578T cells (n=3; 48 h). **P<0.01 and ***P < 0.001 vs. control. CEP, cepharanthine; ns, not significant.

    Journal: Molecular Medicine Reports

    Article Title: Cepharanthine inhibits lysosomes and induces apoptosis in triple-negative breast cancer cells

    doi: 10.3892/mmr.2026.13899

    Figure Lengend Snippet: CEP induces apoptosis in triple-negative breast cancer cells. Flow cytometric quantification of apoptosis induced by CEP in (A) MDA-MB-231 and (B) Hs578T cells (n=3; 48 h). **P<0.01 and ***P < 0.001 vs. control. CEP, cepharanthine; ns, not significant.

    Article Snippet: The TNBC cell lines MDA-MB-231 (cat. no. CL-0150; Procell Life Science & Technology Co., Ltd.) and Hs578T (cat. no. CL-0114; Procell Life Science & Technology Co., Ltd.) were cultured in high-glucose DMEM medium (cat. no. C11965500BT; Gibco; Thermo Fisher Scientific, Inc.), supplemented with 10% fetal bovine serum (cat. no. 164210; Procell Life Science & Technology Co., Ltd.) and 1% penicillin/streptomycin (cat. no. 15140122; Gibco; Thermo Fisher Scientific, Inc.).

    Techniques: Control

    CEP induces ΔΨm loss in triple-negative breast cancer cells. (A) MDA-MB-231 (10 µM; n=3; 24 h) and (B) Hs578T cells (4 µM; n=3; 24 h). Scale bar, 100 µM. CEP, cepharanthine.

    Journal: Molecular Medicine Reports

    Article Title: Cepharanthine inhibits lysosomes and induces apoptosis in triple-negative breast cancer cells

    doi: 10.3892/mmr.2026.13899

    Figure Lengend Snippet: CEP induces ΔΨm loss in triple-negative breast cancer cells. (A) MDA-MB-231 (10 µM; n=3; 24 h) and (B) Hs578T cells (4 µM; n=3; 24 h). Scale bar, 100 µM. CEP, cepharanthine.

    Article Snippet: The TNBC cell lines MDA-MB-231 (cat. no. CL-0150; Procell Life Science & Technology Co., Ltd.) and Hs578T (cat. no. CL-0114; Procell Life Science & Technology Co., Ltd.) were cultured in high-glucose DMEM medium (cat. no. C11965500BT; Gibco; Thermo Fisher Scientific, Inc.), supplemented with 10% fetal bovine serum (cat. no. 164210; Procell Life Science & Technology Co., Ltd.) and 1% penicillin/streptomycin (cat. no. 15140122; Gibco; Thermo Fisher Scientific, Inc.).

    Techniques:

    CEP upregulates NOXA and downregulates Bcl-2 expression in triple-negative breast cancer cells. CEP upregulated NOXA and downregulated Bcl-2 expression in (A) MDA-MB-231 cells (n=3; 24 h) and (B) Hs578T cells (n=3; 24 h). *P<0.05, **P<0.01 and ***P<0.001 vs. control. CEP, cepharanthine; NOXA, phorbol-12-myristate-13-acetate-induced protein 1; ns, not significant.

    Journal: Molecular Medicine Reports

    Article Title: Cepharanthine inhibits lysosomes and induces apoptosis in triple-negative breast cancer cells

    doi: 10.3892/mmr.2026.13899

    Figure Lengend Snippet: CEP upregulates NOXA and downregulates Bcl-2 expression in triple-negative breast cancer cells. CEP upregulated NOXA and downregulated Bcl-2 expression in (A) MDA-MB-231 cells (n=3; 24 h) and (B) Hs578T cells (n=3; 24 h). *P<0.05, **P<0.01 and ***P<0.001 vs. control. CEP, cepharanthine; NOXA, phorbol-12-myristate-13-acetate-induced protein 1; ns, not significant.

    Article Snippet: The TNBC cell lines MDA-MB-231 (cat. no. CL-0150; Procell Life Science & Technology Co., Ltd.) and Hs578T (cat. no. CL-0114; Procell Life Science & Technology Co., Ltd.) were cultured in high-glucose DMEM medium (cat. no. C11965500BT; Gibco; Thermo Fisher Scientific, Inc.), supplemented with 10% fetal bovine serum (cat. no. 164210; Procell Life Science & Technology Co., Ltd.) and 1% penicillin/streptomycin (cat. no. 15140122; Gibco; Thermo Fisher Scientific, Inc.).

    Techniques: Expressing, Control

    Proteomic profiling of MDA-MB-231 cells following CEP treatment. (A) The 20 most significantly downregulated Gene Ontology cellular components with CEP treatment. (B) Significantly downregulated Kyoto Encyclopedia of Genes and Genomes pathways with CEP treatment. CEP, cepharanthine.

    Journal: Molecular Medicine Reports

    Article Title: Cepharanthine inhibits lysosomes and induces apoptosis in triple-negative breast cancer cells

    doi: 10.3892/mmr.2026.13899

    Figure Lengend Snippet: Proteomic profiling of MDA-MB-231 cells following CEP treatment. (A) The 20 most significantly downregulated Gene Ontology cellular components with CEP treatment. (B) Significantly downregulated Kyoto Encyclopedia of Genes and Genomes pathways with CEP treatment. CEP, cepharanthine.

    Article Snippet: The TNBC cell lines MDA-MB-231 (cat. no. CL-0150; Procell Life Science & Technology Co., Ltd.) and Hs578T (cat. no. CL-0114; Procell Life Science & Technology Co., Ltd.) were cultured in high-glucose DMEM medium (cat. no. C11965500BT; Gibco; Thermo Fisher Scientific, Inc.), supplemented with 10% fetal bovine serum (cat. no. 164210; Procell Life Science & Technology Co., Ltd.) and 1% penicillin/streptomycin (cat. no. 15140122; Gibco; Thermo Fisher Scientific, Inc.).

    Techniques:

    CEP treatment activates TFEB in triple-negative breast cancer cells. (A) CEP triggers TFEB nuclear translocation in MDA-MB-231 cells (10 µM; 24 h). (B) CEP triggers TFEB nuclear translocation in Hs578T cells (4 µM; 24 h). Scale bar, 25 µm; n=5. **P<0.01 vs. control. TFEB, transcription factor EB; CEP, cepharanthine.

    Journal: Molecular Medicine Reports

    Article Title: Cepharanthine inhibits lysosomes and induces apoptosis in triple-negative breast cancer cells

    doi: 10.3892/mmr.2026.13899

    Figure Lengend Snippet: CEP treatment activates TFEB in triple-negative breast cancer cells. (A) CEP triggers TFEB nuclear translocation in MDA-MB-231 cells (10 µM; 24 h). (B) CEP triggers TFEB nuclear translocation in Hs578T cells (4 µM; 24 h). Scale bar, 25 µm; n=5. **P<0.01 vs. control. TFEB, transcription factor EB; CEP, cepharanthine.

    Article Snippet: The TNBC cell lines MDA-MB-231 (cat. no. CL-0150; Procell Life Science & Technology Co., Ltd.) and Hs578T (cat. no. CL-0114; Procell Life Science & Technology Co., Ltd.) were cultured in high-glucose DMEM medium (cat. no. C11965500BT; Gibco; Thermo Fisher Scientific, Inc.), supplemented with 10% fetal bovine serum (cat. no. 164210; Procell Life Science & Technology Co., Ltd.) and 1% penicillin/streptomycin (cat. no. 15140122; Gibco; Thermo Fisher Scientific, Inc.).

    Techniques: Translocation Assay, Control

    CEP does not induce LMP, increase lysosomal pH or destabilize lysosomal membrane-bound enzymes in triple-negative breast cancer cells. (A) CEP does not induce LMP, as evidenced by a dispersion of dextran, in MDA-MB-231 (10 µM; 24 h) and Hs578T cells (4 µM; 24 h). Scale bar, 25 µm. (B) CEP does not elevate lysosomal pH in the MDA-MB-231 (10 µM; 24 h) and Hs578T cell lines (4 µM; 24 h). Scale bar, 25 µm. (C) CEP does not induce lysosomal membrane-bound enzymes degradation in the MDA-MB-231 (10 µM; n=3; 24 h) and Hs578T cell lines (4 µM; n=3; 24 h). CEP, cepharanthine; ASAH1, acid ceramidase; SMPD1, sphingomyelin phosphodiesterase; ns, not significant.

    Journal: Molecular Medicine Reports

    Article Title: Cepharanthine inhibits lysosomes and induces apoptosis in triple-negative breast cancer cells

    doi: 10.3892/mmr.2026.13899

    Figure Lengend Snippet: CEP does not induce LMP, increase lysosomal pH or destabilize lysosomal membrane-bound enzymes in triple-negative breast cancer cells. (A) CEP does not induce LMP, as evidenced by a dispersion of dextran, in MDA-MB-231 (10 µM; 24 h) and Hs578T cells (4 µM; 24 h). Scale bar, 25 µm. (B) CEP does not elevate lysosomal pH in the MDA-MB-231 (10 µM; 24 h) and Hs578T cell lines (4 µM; 24 h). Scale bar, 25 µm. (C) CEP does not induce lysosomal membrane-bound enzymes degradation in the MDA-MB-231 (10 µM; n=3; 24 h) and Hs578T cell lines (4 µM; n=3; 24 h). CEP, cepharanthine; ASAH1, acid ceramidase; SMPD1, sphingomyelin phosphodiesterase; ns, not significant.

    Article Snippet: The TNBC cell lines MDA-MB-231 (cat. no. CL-0150; Procell Life Science & Technology Co., Ltd.) and Hs578T (cat. no. CL-0114; Procell Life Science & Technology Co., Ltd.) were cultured in high-glucose DMEM medium (cat. no. C11965500BT; Gibco; Thermo Fisher Scientific, Inc.), supplemented with 10% fetal bovine serum (cat. no. 164210; Procell Life Science & Technology Co., Ltd.) and 1% penicillin/streptomycin (cat. no. 15140122; Gibco; Thermo Fisher Scientific, Inc.).

    Techniques: Membrane, Dispersion

    CEP binds to and inhibits lysosomal enzymes. (A) Structurally altered peptides in the MDA-MB-231 cell line upon CEP treatment (10 µM, 1 h; FC >1.5 or <0.667, false discovery rate <1, P<0.01; n=3). (B) CEP treatment suppresses the maturation of CTSB and CTSD (24 h). *P<0.05, **P<0.01 and ***P<0.001 vs. control. CEP, cepharanthine; FC, fold change; CTSD, cathepsin D; CTSB, cathepsin B; pro-CTSB pro-cathepsin B; pro-CTSD, pro-cathepsin D; i-CTSB, inactive cathepsin B; m-CTSB, mature cathepsin B; m-CTSD, mature cathepsin D.

    Journal: Molecular Medicine Reports

    Article Title: Cepharanthine inhibits lysosomes and induces apoptosis in triple-negative breast cancer cells

    doi: 10.3892/mmr.2026.13899

    Figure Lengend Snippet: CEP binds to and inhibits lysosomal enzymes. (A) Structurally altered peptides in the MDA-MB-231 cell line upon CEP treatment (10 µM, 1 h; FC >1.5 or <0.667, false discovery rate <1, P<0.01; n=3). (B) CEP treatment suppresses the maturation of CTSB and CTSD (24 h). *P<0.05, **P<0.01 and ***P<0.001 vs. control. CEP, cepharanthine; FC, fold change; CTSD, cathepsin D; CTSB, cathepsin B; pro-CTSB pro-cathepsin B; pro-CTSD, pro-cathepsin D; i-CTSB, inactive cathepsin B; m-CTSB, mature cathepsin B; m-CTSD, mature cathepsin D.

    Article Snippet: The TNBC cell lines MDA-MB-231 (cat. no. CL-0150; Procell Life Science & Technology Co., Ltd.) and Hs578T (cat. no. CL-0114; Procell Life Science & Technology Co., Ltd.) were cultured in high-glucose DMEM medium (cat. no. C11965500BT; Gibco; Thermo Fisher Scientific, Inc.), supplemented with 10% fetal bovine serum (cat. no. 164210; Procell Life Science & Technology Co., Ltd.) and 1% penicillin/streptomycin (cat. no. 15140122; Gibco; Thermo Fisher Scientific, Inc.).

    Techniques: Control