Recombinant:Article Title: 5' UTR length shapes alternative N-terminal protein isoforms across cancers and in rare disease.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HeLa cells ATCC CVCL_0030 HEK293T cells ATCC CVCL_0063 Recombinant DNA TRE3G: Annotated human AKR7A2 5′ UTR-CDS-EGFP Ly et al, 2025 pJL597 TRE3G: Truncated AKR7A2-EGFP Ly et al, 2025 pJL598 TRE3G: Annotated mouse AKR7A2 5′ UTR-CDS-EGFP This study pJL872 TRE3G: Annotated human ALDH9A1 CDS-EGFP Ly et al, 2025 pJL806 TRE3G: Orangutan ALDH9A1 5′ UTR-CDSEGFP This study pJL1046 TRE3G: CFD 5′ UTR-CDSEGFP This study pJL569 TRE3G: truncated CFDEGFP This study pJL570 TRE3G: CFD1-39-EGFP This study pJL669 NES-GFP dual start codon reporter This study pJL939 Antibodies Anti-GFP Roche 11814460001 (AB_390913) Anti-α-tubulin Abcam ab52866 (AB_869989) IRDye 680RD Goat antiRabbit LI-COR 926-68071 (AB_10956166) IRDye 680RD Goat antiMouse LI-COR 926-68070 (AB_10956588) IRDye 800CW Goat antiRabbit LI-COR 926-32211 (AB_621843) IRDye 800CW Goat antiMouse LI-COR 926-32210 (AB_621842) Oligonucleotides and other sequence-based reagents Template-switching oligo Ly et al, 2025 oJL1137 AKR7A2 RACE oligo This study oJL1466 AKR7A2 nested RACE oligo This study oJL1467 Chemicals, enzymes, and other reagents MycoAlert Mycoplasma Detection Kit Lonza LT07-418 Maxima First Strand cDNA Synthesis Kit Thermo Fisher Scientific K1641 Lipofectamine 2000 Thermo Fisher Scientific 11668027 Lipofectamine MessengerMAX Thermo Fisher Scientific LMRNA008 HiScribe T7 ARCA mRNA Kit (with tailing) NEB E2060 Reagent/resource Reference or source Identifier or catalog number Monarch RNA Cleanup Kit NEB T2040 EconoSpin All-in-1 Mini Spin Columns Epoch Life Science 1920-250 Template Switching RT Enzyme Mix NEB M0466 TRI Reagent Invitrogen AM9738 S-Trap micro columns Protifi C002‐MICRO‐0080PK Trypsin Promega V5111 TMT10plex kit Thermo Fisher Scientific 90111 Pierce High-pH peptide fractionation kit Thermo Fisher Scientific 84868 Software CellProfiler Carpenter et al, 2006 https://cellprofiler.org Kallisto Bray et al, 2016 https://pachterlab.github.io/ kallisto fgsea (R package) Bioconductor STAR aligner Dobin et al, 2013 https://github.com/ alexdobin/STAR bedtools Quinlan and Hall, 2010 deepTools Ramirez et al, 2014 IGV Thorvaldsdottir et al, 2013 https://software. .. broadinstitute.org/software/ igv/ Proteome Discoverer Thermo Fisher Scientific 5′ UTR ClinVar analysis This study https://github.com/ cheeseman-lab/5-utr-clinvarmutations
Sequencing:Article Title: 5' UTR length shapes alternative N-terminal protein isoforms across cancers and in rare disease.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HeLa cells ATCC CVCL_0030 HEK293T cells ATCC CVCL_0063 Recombinant DNA TRE3G: Annotated human AKR7A2 5′ UTR-CDS-EGFP Ly et al, 2025 pJL597 TRE3G: Truncated AKR7A2-EGFP Ly et al, 2025 pJL598 TRE3G: Annotated mouse AKR7A2 5′ UTR-CDS-EGFP This study pJL872 TRE3G: Annotated human ALDH9A1 CDS-EGFP Ly et al, 2025 pJL806 TRE3G: Orangutan ALDH9A1 5′ UTR-CDSEGFP This study pJL1046 TRE3G: CFD 5′ UTR-CDSEGFP This study pJL569 TRE3G: truncated CFDEGFP This study pJL570 TRE3G: CFD1-39-EGFP This study pJL669 NES-GFP dual start codon reporter This study pJL939 Antibodies Anti-GFP Roche 11814460001 (AB_390913) Anti-α-tubulin Abcam ab52866 (AB_869989) IRDye 680RD Goat antiRabbit LI-COR 926-68071 (AB_10956166) IRDye 680RD Goat antiMouse LI-COR 926-68070 (AB_10956588) IRDye 800CW Goat antiRabbit LI-COR 926-32211 (AB_621843) IRDye 800CW Goat antiMouse LI-COR 926-32210 (AB_621842) Oligonucleotides and other sequence-based reagents Template-switching oligo Ly et al, 2025 oJL1137 AKR7A2 RACE oligo This study oJL1466 AKR7A2 nested RACE oligo This study oJL1467 Chemicals, enzymes, and other reagents MycoAlert Mycoplasma Detection Kit Lonza LT07-418 Maxima First Strand cDNA Synthesis Kit Thermo Fisher Scientific K1641 Lipofectamine 2000 Thermo Fisher Scientific 11668027 Lipofectamine MessengerMAX Thermo Fisher Scientific LMRNA008 HiScribe T7 ARCA mRNA Kit (with tailing) NEB E2060 Reagent/resource Reference or source Identifier or catalog number Monarch RNA Cleanup Kit NEB T2040 EconoSpin All-in-1 Mini Spin Columns Epoch Life Science 1920-250 Template Switching RT Enzyme Mix NEB M0466 TRI Reagent Invitrogen AM9738 S-Trap micro columns Protifi C002‐MICRO‐0080PK Trypsin Promega V5111 TMT10plex kit Thermo Fisher Scientific 90111 Pierce High-pH peptide fractionation kit Thermo Fisher Scientific 84868 Software CellProfiler Carpenter et al, 2006 https://cellprofiler.org Kallisto Bray et al, 2016 https://pachterlab.github.io/ kallisto fgsea (R package) Bioconductor STAR aligner Dobin et al, 2013 https://github.com/ alexdobin/STAR bedtools Quinlan and Hall, 2010 deepTools Ramirez et al, 2014 IGV Thorvaldsdottir et al, 2013 https://software. .. broadinstitute.org/software/ igv/ Proteome Discoverer Thermo Fisher Scientific 5′ UTR ClinVar analysis This study https://github.com/ cheeseman-lab/5-utr-clinvarmutations
cDNA Synthesis:Article Title: 5' UTR length shapes alternative N-terminal protein isoforms across cancers and in rare disease.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HeLa cells ATCC CVCL_0030 HEK293T cells ATCC CVCL_0063 Recombinant DNA TRE3G: Annotated human AKR7A2 5′ UTR-CDS-EGFP Ly et al, 2025 pJL597 TRE3G: Truncated AKR7A2-EGFP Ly et al, 2025 pJL598 TRE3G: Annotated mouse AKR7A2 5′ UTR-CDS-EGFP This study pJL872 TRE3G: Annotated human ALDH9A1 CDS-EGFP Ly et al, 2025 pJL806 TRE3G: Orangutan ALDH9A1 5′ UTR-CDSEGFP This study pJL1046 TRE3G: CFD 5′ UTR-CDSEGFP This study pJL569 TRE3G: truncated CFDEGFP This study pJL570 TRE3G: CFD1-39-EGFP This study pJL669 NES-GFP dual start codon reporter This study pJL939 Antibodies Anti-GFP Roche 11814460001 (AB_390913) Anti-α-tubulin Abcam ab52866 (AB_869989) IRDye 680RD Goat antiRabbit LI-COR 926-68071 (AB_10956166) IRDye 680RD Goat antiMouse LI-COR 926-68070 (AB_10956588) IRDye 800CW Goat antiRabbit LI-COR 926-32211 (AB_621843) IRDye 800CW Goat antiMouse LI-COR 926-32210 (AB_621842) Oligonucleotides and other sequence-based reagents Template-switching oligo Ly et al, 2025 oJL1137 AKR7A2 RACE oligo This study oJL1466 AKR7A2 nested RACE oligo This study oJL1467 Chemicals, enzymes, and other reagents MycoAlert Mycoplasma Detection Kit Lonza LT07-418 Maxima First Strand cDNA Synthesis Kit Thermo Fisher Scientific K1641 Lipofectamine 2000 Thermo Fisher Scientific 11668027 Lipofectamine MessengerMAX Thermo Fisher Scientific LMRNA008 HiScribe T7 ARCA mRNA Kit (with tailing) NEB E2060 Reagent/resource Reference or source Identifier or catalog number Monarch RNA Cleanup Kit NEB T2040 EconoSpin All-in-1 Mini Spin Columns Epoch Life Science 1920-250 Template Switching RT Enzyme Mix NEB M0466 TRI Reagent Invitrogen AM9738 S-Trap micro columns Protifi C002‐MICRO‐0080PK Trypsin Promega V5111 TMT10plex kit Thermo Fisher Scientific 90111 Pierce High-pH peptide fractionation kit Thermo Fisher Scientific 84868 Software CellProfiler Carpenter et al, 2006 https://cellprofiler.org Kallisto Bray et al, 2016 https://pachterlab.github.io/ kallisto fgsea (R package) Bioconductor STAR aligner Dobin et al, 2013 https://github.com/ alexdobin/STAR bedtools Quinlan and Hall, 2010 deepTools Ramirez et al, 2014 IGV Thorvaldsdottir et al, 2013 https://software. .. broadinstitute.org/software/ igv/ Proteome Discoverer Thermo Fisher Scientific 5′ UTR ClinVar analysis This study https://github.com/ cheeseman-lab/5-utr-clinvarmutations
Peptide Fractionation:Article Title: 5' UTR length shapes alternative N-terminal protein isoforms across cancers and in rare disease.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HeLa cells ATCC CVCL_0030 HEK293T cells ATCC CVCL_0063 Recombinant DNA TRE3G: Annotated human AKR7A2 5′ UTR-CDS-EGFP Ly et al, 2025 pJL597 TRE3G: Truncated AKR7A2-EGFP Ly et al, 2025 pJL598 TRE3G: Annotated mouse AKR7A2 5′ UTR-CDS-EGFP This study pJL872 TRE3G: Annotated human ALDH9A1 CDS-EGFP Ly et al, 2025 pJL806 TRE3G: Orangutan ALDH9A1 5′ UTR-CDSEGFP This study pJL1046 TRE3G: CFD 5′ UTR-CDSEGFP This study pJL569 TRE3G: truncated CFDEGFP This study pJL570 TRE3G: CFD1-39-EGFP This study pJL669 NES-GFP dual start codon reporter This study pJL939 Antibodies Anti-GFP Roche 11814460001 (AB_390913) Anti-α-tubulin Abcam ab52866 (AB_869989) IRDye 680RD Goat antiRabbit LI-COR 926-68071 (AB_10956166) IRDye 680RD Goat antiMouse LI-COR 926-68070 (AB_10956588) IRDye 800CW Goat antiRabbit LI-COR 926-32211 (AB_621843) IRDye 800CW Goat antiMouse LI-COR 926-32210 (AB_621842) Oligonucleotides and other sequence-based reagents Template-switching oligo Ly et al, 2025 oJL1137 AKR7A2 RACE oligo This study oJL1466 AKR7A2 nested RACE oligo This study oJL1467 Chemicals, enzymes, and other reagents MycoAlert Mycoplasma Detection Kit Lonza LT07-418 Maxima First Strand cDNA Synthesis Kit Thermo Fisher Scientific K1641 Lipofectamine 2000 Thermo Fisher Scientific 11668027 Lipofectamine MessengerMAX Thermo Fisher Scientific LMRNA008 HiScribe T7 ARCA mRNA Kit (with tailing) NEB E2060 Reagent/resource Reference or source Identifier or catalog number Monarch RNA Cleanup Kit NEB T2040 EconoSpin All-in-1 Mini Spin Columns Epoch Life Science 1920-250 Template Switching RT Enzyme Mix NEB M0466 TRI Reagent Invitrogen AM9738 S-Trap micro columns Protifi C002‐MICRO‐0080PK Trypsin Promega V5111 TMT10plex kit Thermo Fisher Scientific 90111 Pierce High-pH peptide fractionation kit Thermo Fisher Scientific 84868 Software CellProfiler Carpenter et al, 2006 https://cellprofiler.org Kallisto Bray et al, 2016 https://pachterlab.github.io/ kallisto fgsea (R package) Bioconductor STAR aligner Dobin et al, 2013 https://github.com/ alexdobin/STAR bedtools Quinlan and Hall, 2010 deepTools Ramirez et al, 2014 IGV Thorvaldsdottir et al, 2013 https://software. .. broadinstitute.org/software/ igv/ Proteome Discoverer Thermo Fisher Scientific 5′ UTR ClinVar analysis This study https://github.com/ cheeseman-lab/5-utr-clinvarmutations
Software:Article Title: 5' UTR length shapes alternative N-terminal protein isoforms across cancers and in rare disease.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HeLa cells ATCC CVCL_0030 HEK293T cells ATCC CVCL_0063 Recombinant DNA TRE3G: Annotated human AKR7A2 5′ UTR-CDS-EGFP Ly et al, 2025 pJL597 TRE3G: Truncated AKR7A2-EGFP Ly et al, 2025 pJL598 TRE3G: Annotated mouse AKR7A2 5′ UTR-CDS-EGFP This study pJL872 TRE3G: Annotated human ALDH9A1 CDS-EGFP Ly et al, 2025 pJL806 TRE3G: Orangutan ALDH9A1 5′ UTR-CDSEGFP This study pJL1046 TRE3G: CFD 5′ UTR-CDSEGFP This study pJL569 TRE3G: truncated CFDEGFP This study pJL570 TRE3G: CFD1-39-EGFP This study pJL669 NES-GFP dual start codon reporter This study pJL939 Antibodies Anti-GFP Roche 11814460001 (AB_390913) Anti-α-tubulin Abcam ab52866 (AB_869989) IRDye 680RD Goat antiRabbit LI-COR 926-68071 (AB_10956166) IRDye 680RD Goat antiMouse LI-COR 926-68070 (AB_10956588) IRDye 800CW Goat antiRabbit LI-COR 926-32211 (AB_621843) IRDye 800CW Goat antiMouse LI-COR 926-32210 (AB_621842) Oligonucleotides and other sequence-based reagents Template-switching oligo Ly et al, 2025 oJL1137 AKR7A2 RACE oligo This study oJL1466 AKR7A2 nested RACE oligo This study oJL1467 Chemicals, enzymes, and other reagents MycoAlert Mycoplasma Detection Kit Lonza LT07-418 Maxima First Strand cDNA Synthesis Kit Thermo Fisher Scientific K1641 Lipofectamine 2000 Thermo Fisher Scientific 11668027 Lipofectamine MessengerMAX Thermo Fisher Scientific LMRNA008 HiScribe T7 ARCA mRNA Kit (with tailing) NEB E2060 Reagent/resource Reference or source Identifier or catalog number Monarch RNA Cleanup Kit NEB T2040 EconoSpin All-in-1 Mini Spin Columns Epoch Life Science 1920-250 Template Switching RT Enzyme Mix NEB M0466 TRI Reagent Invitrogen AM9738 S-Trap micro columns Protifi C002‐MICRO‐0080PK Trypsin Promega V5111 TMT10plex kit Thermo Fisher Scientific 90111 Pierce High-pH peptide fractionation kit Thermo Fisher Scientific 84868 Software CellProfiler Carpenter et al, 2006 https://cellprofiler.org Kallisto Bray et al, 2016 https://pachterlab.github.io/ kallisto fgsea (R package) Bioconductor STAR aligner Dobin et al, 2013 https://github.com/ alexdobin/STAR bedtools Quinlan and Hall, 2010 deepTools Ramirez et al, 2014 IGV Thorvaldsdottir et al, 2013 https://software. .. broadinstitute.org/software/ igv/ Proteome Discoverer Thermo Fisher Scientific 5′ UTR ClinVar analysis This study https://github.com/ cheeseman-lab/5-utr-clinvarmutations
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