bz-x810 fluorescence microscope (KEYENCE)
90
Structured Review
KEYENCE
bz-x810 fluorescence microscope
Bz X810 Fluorescence Microscope, supplied by KEYENCE, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bz-x810+fluorescence+microscope/fluorescence+microscope+bz+9000/pmc12270548-126-6-9
Average 90 stars, based on 1 article reviews
Bz X810 Fluorescence Microscope, supplied by KEYENCE, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bz-x810+fluorescence+microscope/fluorescence+microscope+bz+9000/pmc12270548-126-6-9
Average 90 stars, based on 1 article reviews
bz-x810 fluorescence microscope - by Bioz Stars,
2026-10
90/100 stars
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Fluorescence:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: Microscopy:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: Staining:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: Modification:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: RNA Sequencing:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: Multiplex Assay:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: Recombinant:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: Plasmid Preparation:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: Software:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: Spectrophotometry:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: Blocking Assay:Article Title: Controlled liquid-liquid phase separation via the simulation-guided, targeted engineering of the RNA-binding protein PARCL Article Snippet: Condensation formation was observed by fluorescence microscopy using a Article Title: Discovery of effectors for casein kinase signaling in the African trypanosome. Article Snippet: Images were acquired and analyzed with a Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Raw RNA-seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Raw eCLIP- seq data (accession number PRJNA1143587) This paper https://www.ncbi.nlm.nih.gov/ bioproject/PRJNA1143587 Experimental models: Organisms/strains Plasmodium falciparum NF54 Nasamu et al.23 NF54::pCRISPRINT Inducible PfRAP03-HA line This paper N/A Inducible PfRAP08-HA line This paper N/A Plasmodium falciparum 3D7 MR4 3D7 Oligonucleotides NEBNext Multiplex Oligos for Illumina NEB Cat#E6609S Oligos from RBP-eCLIP kit Eclipsebio Cat#143637 Primers and oligonucleotides used This paper Table S5 Recombinant DNA pSN053 linear vector Nasamu et al.23 N/A Software and algorithms Bowtie 2 version 2.5.3 Langmead et al.49 https://bowtie-bio.sourceforge.net/ bowtie2/index.shtml Samtools version 1.19.2 Li et al.50 http://samtools.sourceforge.net/ IGV (Integrative Genomic Viewer) version 2.18.4 Thorvaldsdóttir et al.51 http://software.broadinstitute. org/software/igv/home Image Lab version 5 Bio-Rad N/A ImageJ N/A https://imagej.net/ij/ FastQC version 0.12.1 Andrews et al.52 http://www.bioinformatics. babraham.ac.uk/projects/ PlasmoDB VEuPathDB https://plasmodb.org/plasmo/app cutadapt version 4.6 Martin et al.53 https://cutadapt.readthedocs.io/en/stable/ HISAT2 version 2.2.1 Kim et al.54 https://daehwankimlab.github.io/hisat2/ HTSeq version 2.0.5 Anders et al.55 https://htseq.readthedocs.io/en/latest/ DESeq2 (R package) version 1.42.1 Love et al.56 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnhancedVolcano (R package) N/A https://github.com/kevinblighe/ EnhancedVolcano RawDistiller version 1.0 In-house software N/A ProLuCID version 1.3.3 Xu et al.57 N/A DTASelect version 1.9 Tabb et al.58 N/A swallow In-house software https://github.com/tzw-wen/kite Contrast version 1.9 Tabb et al.58 sandmartin In-house software https://github.com/tzw-wen/kite NSAF7x64 In-house software https://github.com/tzw-wen/kite/tree/ master/windowsapp/NSAF7x64 QPROT Choi et al.59 https://sourceforge.net/projects/qprot/ Piranha version 1.2.1 N/A http://smithlabresearch.org/software/piranha/ ChIPseeker version 1.24.0 (R package) N/A https://www.bioconductor.org/packages/ release/bioc/html/ChIPseeker.html Other S220 Focused-ultrasonicator Covaris S220 ChemiDocTM BioRad N/A Keyence BZ-X810 fluorescence microscope Keyence BZ-X810 Fluorometer Spectrophotometer DeNovix DS-11 FX+ (Continued on next page) Cell Reports 44, 115928, July 22, 2025 13 Article Title: Protocol for using MYOD1 -transduced human urine-derived cells as a predictive platform for exon skipping therapy in Duchenne muscular dystrophy Article Snippet: Note: Since UDCs are very sensitive to triton-X, the reaction time with 0.1% triton-X should not exceed 5 min. c. Block the cells with 10% goat serum (Thermo Fisher Scientific) diluted in PBS for 15 min at 37°C. d. Incubate the cells with primary rabbit antibody to dystrophin (1:500; Abcam, ab15277) in PBS for 8–16 h at 4°C. e. After washing the cells with PBS over three times, incubate them with a secondary antibody as Alexa Fluor 594 goat anti-rabbit IgG (1:300; Molecular Probes) in PBS for 30 min at 15°C–30°C. f. Wash the cells with PBS over three times, and incubate them with 1 mg/mL of DAPI (1:20,000; Dojindo) in PBS for 10 min at 15°C–30°C. g. Observe the Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: Images were captured using a Article Title: The flap endonuclease-1 promotes cellular tolerance to a chain-terminating nucleoside analog, alovudine, by counteracting the toxic effect of 53BP1 Article Snippet: The images were captured using a Article Title: Expression of Netrin-1 in the developing mouse heart. Article Snippet: Images were taken using the Article Title: RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum. Article Snippet: |