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    Bio-Rad resource source identifier iscript cdna synthesis biorad
    Resource Source Identifier Iscript Cdna Synthesis Biorad, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 6678 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/resource+source+identifier/IScript+C+DNA+Synthesis+Kit/pm42815461-276-2-8
    Average 99 stars, based on 6678 article reviews
    resource source identifier iscript cdna synthesis biorad - by Bioz Stars, 2026-10
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    Membrane:


    Article Title: The hidden bacterial microproteome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Escherichia coli strain MG1655 minil::cmR Nadim Majdalani NM400 E. coli K-12 F- l- ilvG- rfb-50 rph-1 Lab stock MG1655 E. coli MG1655 mini-l:cat N. Majdalani NM400 E. coli MG1655 ORF.34481-SPA::kan This study GSO1268 E. coli MG1655 ORF.34913-SPA::kan This study GSO1269 E. coli MG1655 ORF.89829-SPA::kan This study GSO1270 E. coli MG1655 ORF.24169-SPA::kan This study GSO1271 E. coli MG1655 ORF.60640-SPA::kan This study GSO1272 E. coli MG1655 ORF.27988-SPA::kan This study GSO1273 E. coli MG1655 ORF.50946-SPA::kan This study GSO1274 E. coli MG1655 ORF.40689-SPA::kan This study GSO1275 E. coli MG1655 ORF.35968-SPA::kan This study GSO1276 E. coli MG1655 ORF.63424-SPA::kan This study GSO1277 E. coli MG1655 ORF.78845-SPA::kan This study GSO1278 E. coli MG1655 ORF.18101-SPA::kan This study GSO1279 E. coli MG1655 ORF.92637-SPA::kan This study GSO1280 E. coli MG1655 ORF.59530-SPA::kan This study GSO1281 E. coli MG1655 ORF.8970-SPA::kan This study GSO1282 E. coli MG1655 ORF.3078-SPA::kan This study GSO1283 E. coli MG1655 ybhL-SPA::kan This study GSO1284 E. coli MG1655 ybhL-SPA::kan/pBAD24 This study GSO1285 E. coli MG1655 ybhL-SPA::kan/pBAD24 ORF.3078 This study GSO1286 Chemicals, peptides, and recombinant proteins Sodium Chloride Aventor Cat#7647-14-5 Bacto Tryptone Thermo Fisher Scientific Cat#211705 Bacto Yeast Extract Thermo Fisher Scientific Cat#2122750 Potassium Sulfate Sigma- Aldrich Cat#7778-80-5 Ammonium Sulfate Sigma- Aldrich Cat# 7783-20-2 Potassium Phosphate Monobasic Sigma- Aldrich Cat#7778-77-0 Casamino Acids Aventor Cat#97063-378 Glycerol Chem-Impex International Cat#30144 Vitamin B1 KD Medical Cat#CAC-5360 Tris Buffer pH 7.5 KD Medical Cat#RGF-3370 Potassium Chloride KD Medical Cat#CAC-5321 Tris Glycine SDS 10X KD Medical Cat#RGF-3390 10% SDS KD Medical Cat#RGF-3230 10 X Phosphate-Buffered Saline (PBS) Corning Cat#46-013-M Quick-Load Purple 1KB Plus DNA Ladder New England Biolabs Cat#NO550S Q5 High- Fidelity 2X Master Mix New England Biolabs Cat#MO492S Gel Loading Dye (6X) New England Biolabs Cat#B7024S Fisher BioReagents EZ-RUN Prestained Rec Protein Ladder Thermo Fisher Scientific Cat#BP3603-500 (Continued on next page) Molecular Cell 85, 1–18.e1–e6, March 6, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER 4-20% Mini-PROTEAN TGX Precast Protein Gel BIO-RAD Cat#4561096 Laemmli SDS sample buffer reducing (6X) Thermo Fisher Scientific Cat#J61337.AD Nitrocellulose membrane Filter paper Invitrogen Cat#LC2000 Western Blotting Filter Paper Thermo Fisher Scientific Cat#88600 Blotting-Grade Blocker BIO-RAD Cat#1706404 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34095 SuperSignal West Pico Plus Chemiluminescent Substrate Thermo Fisher Scientific Cat#34577 Monoclonal ANTI-FLAG M2Peroxidase (mouse) Sigma- Aldrich Cat# A8592, RRID:AB_439702 20% Arabinose KD Medical Cat#CAC-5020 Critical commercial assays Gibson Assembly Cloning Kit New England Biolabs Cat#E2621S Deposited data All original data and code produced in this work This paper https://zenodo.org/records/10672687 Original code produced in this study This paper https://github.com/IgorFesenko/ prokariotic_smORFs Accompanying interactive Colab Notebook This paper https://colab.research.google.com/github/ IgorFesenko/prokariotic_smORFs/blob/ main/ismORFs_resource.ipynb Software and algorithms CD-HIT Li and Godzik et al.103 https://github.com/weizhongli/cdhit RNAcode Washietl et al.33 https://github.com/ViennaRNA/RNAcode MEGA X Kumar et al.104 https://www.megasoftware.net/ MAFFT v7.475 Katoh and Standley105 https://mafft.cbrc.jp/alignment/software/ HH-Suite Steinegger et al.65 https://github.com/soedinglab/hh-suite orfipy Singh and Wurtele106 https://github.com/urmi-21/orfipy SmORFinder Durrant and Bhatt36 https://github.com/bhattlab/SmORFinder Biopython Cock et al.107 https://biopython.org/ IQ-Tree Nguyen et al.108 http://www.iqtree.org/ InterProscan 5.60–92.0 Quevillon et al.72 https://github.com/ebi-pf-team/ interproscan SibeliaZ Minkin and Medvedev44 https://github.com/medvedevgroup/ SibeliaZ SignalP 6 Teufel et al.109 https://github.com/fteufel/signalp-6.0/ blob/main/installation_instructions.md NCBI BLAST+ suite Altschul et al.110; Johnson et al.111 https://ftp.ncbi.nlm.nih.gov/blast/ executables/blast+/LATEST/ R The R Project for Statistical Computing https://cran.r-project.org/ Python Python Software Foundation https://www.python.org MMseqs2 Hauser et al.41 https://github.com/soedinglab/MMseqs2 uShuffle Jiang et al.112 https://github.com/guma44/ushuffle trimgalore 0.6.7 Krueger113 https://github.com/FelixKrueger/ TrimGalore bowtie 2-2.5.1 Langmead and Salzberg114 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml HISAT2 2.2.1 Kim et al.115 http://daehwankimlab.github.io/hisat2/ (Continued on next page) e2 Molecular Cell 85, 1–18.e1–e6, March 6, 2025 ..

    Protease Inhibitor:


    Western Blot:


    Article Title: The hidden bacterial microproteome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Escherichia coli strain MG1655 minil::cmR Nadim Majdalani NM400 E. coli K-12 F- l- ilvG- rfb-50 rph-1 Lab stock MG1655 E. coli MG1655 mini-l:cat N. Majdalani NM400 E. coli MG1655 ORF.34481-SPA::kan This study GSO1268 E. coli MG1655 ORF.34913-SPA::kan This study GSO1269 E. coli MG1655 ORF.89829-SPA::kan This study GSO1270 E. coli MG1655 ORF.24169-SPA::kan This study GSO1271 E. coli MG1655 ORF.60640-SPA::kan This study GSO1272 E. coli MG1655 ORF.27988-SPA::kan This study GSO1273 E. coli MG1655 ORF.50946-SPA::kan This study GSO1274 E. coli MG1655 ORF.40689-SPA::kan This study GSO1275 E. coli MG1655 ORF.35968-SPA::kan This study GSO1276 E. coli MG1655 ORF.63424-SPA::kan This study GSO1277 E. coli MG1655 ORF.78845-SPA::kan This study GSO1278 E. coli MG1655 ORF.18101-SPA::kan This study GSO1279 E. coli MG1655 ORF.92637-SPA::kan This study GSO1280 E. coli MG1655 ORF.59530-SPA::kan This study GSO1281 E. coli MG1655 ORF.8970-SPA::kan This study GSO1282 E. coli MG1655 ORF.3078-SPA::kan This study GSO1283 E. coli MG1655 ybhL-SPA::kan This study GSO1284 E. coli MG1655 ybhL-SPA::kan/pBAD24 This study GSO1285 E. coli MG1655 ybhL-SPA::kan/pBAD24 ORF.3078 This study GSO1286 Chemicals, peptides, and recombinant proteins Sodium Chloride Aventor Cat#7647-14-5 Bacto Tryptone Thermo Fisher Scientific Cat#211705 Bacto Yeast Extract Thermo Fisher Scientific Cat#2122750 Potassium Sulfate Sigma- Aldrich Cat#7778-80-5 Ammonium Sulfate Sigma- Aldrich Cat# 7783-20-2 Potassium Phosphate Monobasic Sigma- Aldrich Cat#7778-77-0 Casamino Acids Aventor Cat#97063-378 Glycerol Chem-Impex International Cat#30144 Vitamin B1 KD Medical Cat#CAC-5360 Tris Buffer pH 7.5 KD Medical Cat#RGF-3370 Potassium Chloride KD Medical Cat#CAC-5321 Tris Glycine SDS 10X KD Medical Cat#RGF-3390 10% SDS KD Medical Cat#RGF-3230 10 X Phosphate-Buffered Saline (PBS) Corning Cat#46-013-M Quick-Load Purple 1KB Plus DNA Ladder New England Biolabs Cat#NO550S Q5 High- Fidelity 2X Master Mix New England Biolabs Cat#MO492S Gel Loading Dye (6X) New England Biolabs Cat#B7024S Fisher BioReagents EZ-RUN Prestained Rec Protein Ladder Thermo Fisher Scientific Cat#BP3603-500 (Continued on next page) Molecular Cell 85, 1–18.e1–e6, March 6, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER 4-20% Mini-PROTEAN TGX Precast Protein Gel BIO-RAD Cat#4561096 Laemmli SDS sample buffer reducing (6X) Thermo Fisher Scientific Cat#J61337.AD Nitrocellulose membrane Filter paper Invitrogen Cat#LC2000 Western Blotting Filter Paper Thermo Fisher Scientific Cat#88600 Blotting-Grade Blocker BIO-RAD Cat#1706404 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34095 SuperSignal West Pico Plus Chemiluminescent Substrate Thermo Fisher Scientific Cat#34577 Monoclonal ANTI-FLAG M2Peroxidase (mouse) Sigma- Aldrich Cat# A8592, RRID:AB_439702 20% Arabinose KD Medical Cat#CAC-5020 Critical commercial assays Gibson Assembly Cloning Kit New England Biolabs Cat#E2621S Deposited data All original data and code produced in this work This paper https://zenodo.org/records/10672687 Original code produced in this study This paper https://github.com/IgorFesenko/ prokariotic_smORFs Accompanying interactive Colab Notebook This paper https://colab.research.google.com/github/ IgorFesenko/prokariotic_smORFs/blob/ main/ismORFs_resource.ipynb Software and algorithms CD-HIT Li and Godzik et al.103 https://github.com/weizhongli/cdhit RNAcode Washietl et al.33 https://github.com/ViennaRNA/RNAcode MEGA X Kumar et al.104 https://www.megasoftware.net/ MAFFT v7.475 Katoh and Standley105 https://mafft.cbrc.jp/alignment/software/ HH-Suite Steinegger et al.65 https://github.com/soedinglab/hh-suite orfipy Singh and Wurtele106 https://github.com/urmi-21/orfipy SmORFinder Durrant and Bhatt36 https://github.com/bhattlab/SmORFinder Biopython Cock et al.107 https://biopython.org/ IQ-Tree Nguyen et al.108 http://www.iqtree.org/ InterProscan 5.60–92.0 Quevillon et al.72 https://github.com/ebi-pf-team/ interproscan SibeliaZ Minkin and Medvedev44 https://github.com/medvedevgroup/ SibeliaZ SignalP 6 Teufel et al.109 https://github.com/fteufel/signalp-6.0/ blob/main/installation_instructions.md NCBI BLAST+ suite Altschul et al.110; Johnson et al.111 https://ftp.ncbi.nlm.nih.gov/blast/ executables/blast+/LATEST/ R The R Project for Statistical Computing https://cran.r-project.org/ Python Python Software Foundation https://www.python.org MMseqs2 Hauser et al.41 https://github.com/soedinglab/MMseqs2 uShuffle Jiang et al.112 https://github.com/guma44/ushuffle trimgalore 0.6.7 Krueger113 https://github.com/FelixKrueger/ TrimGalore bowtie 2-2.5.1 Langmead and Salzberg114 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml HISAT2 2.2.1 Kim et al.115 http://daehwankimlab.github.io/hisat2/ (Continued on next page) e2 Molecular Cell 85, 1–18.e1–e6, March 6, 2025 ..

    Strep-tag:


    SYBR Green Assay:


    MTT Assay:


    Bicinchoninic Acid Protein Assay:


    Plasmid Preparation:


    RNA Sequencing:


    RNA HS Assay:


    Reverse Transcription:


    Expressing:

    Article Title: Type I interferons induce guanylate-binding proteins and lysosomal defense in hepatocytes to control malaria.
    Article Snippet: Article Type I interferons induce guanylate-binding proteins and lysosomal defense in hepatocytes to control malaria

    Cloning:

    Article Title: The hidden bacterial microproteome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Escherichia coli strain MG1655 minil::cmR Nadim Majdalani NM400 E. coli K-12 F- l- ilvG- rfb-50 rph-1 Lab stock MG1655 E. coli MG1655 mini-l:cat N. Majdalani NM400 E. coli MG1655 ORF.34481-SPA::kan This study GSO1268 E. coli MG1655 ORF.34913-SPA::kan This study GSO1269 E. coli MG1655 ORF.89829-SPA::kan This study GSO1270 E. coli MG1655 ORF.24169-SPA::kan This study GSO1271 E. coli MG1655 ORF.60640-SPA::kan This study GSO1272 E. coli MG1655 ORF.27988-SPA::kan This study GSO1273 E. coli MG1655 ORF.50946-SPA::kan This study GSO1274 E. coli MG1655 ORF.40689-SPA::kan This study GSO1275 E. coli MG1655 ORF.35968-SPA::kan This study GSO1276 E. coli MG1655 ORF.63424-SPA::kan This study GSO1277 E. coli MG1655 ORF.78845-SPA::kan This study GSO1278 E. coli MG1655 ORF.18101-SPA::kan This study GSO1279 E. coli MG1655 ORF.92637-SPA::kan This study GSO1280 E. coli MG1655 ORF.59530-SPA::kan This study GSO1281 E. coli MG1655 ORF.8970-SPA::kan This study GSO1282 E. coli MG1655 ORF.3078-SPA::kan This study GSO1283 E. coli MG1655 ybhL-SPA::kan This study GSO1284 E. coli MG1655 ybhL-SPA::kan/pBAD24 This study GSO1285 E. coli MG1655 ybhL-SPA::kan/pBAD24 ORF.3078 This study GSO1286 Chemicals, peptides, and recombinant proteins Sodium Chloride Aventor Cat#7647-14-5 Bacto Tryptone Thermo Fisher Scientific Cat#211705 Bacto Yeast Extract Thermo Fisher Scientific Cat#2122750 Potassium Sulfate Sigma- Aldrich Cat#7778-80-5 Ammonium Sulfate Sigma- Aldrich Cat# 7783-20-2 Potassium Phosphate Monobasic Sigma- Aldrich Cat#7778-77-0 Casamino Acids Aventor Cat#97063-378 Glycerol Chem-Impex International Cat#30144 Vitamin B1 KD Medical Cat#CAC-5360 Tris Buffer pH 7.5 KD Medical Cat#RGF-3370 Potassium Chloride KD Medical Cat#CAC-5321 Tris Glycine SDS 10X KD Medical Cat#RGF-3390 10% SDS KD Medical Cat#RGF-3230 10 X Phosphate-Buffered Saline (PBS) Corning Cat#46-013-M Quick-Load Purple 1KB Plus DNA Ladder New England Biolabs Cat#NO550S Q5 High- Fidelity 2X Master Mix New England Biolabs Cat#MO492S Gel Loading Dye (6X) New England Biolabs Cat#B7024S Fisher BioReagents EZ-RUN Prestained Rec Protein Ladder Thermo Fisher Scientific Cat#BP3603-500 (Continued on next page) Molecular Cell 85, 1–18.e1–e6, March 6, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER 4-20% Mini-PROTEAN TGX Precast Protein Gel BIO-RAD Cat#4561096 Laemmli SDS sample buffer reducing (6X) Thermo Fisher Scientific Cat#J61337.AD Nitrocellulose membrane Filter paper Invitrogen Cat#LC2000 Western Blotting Filter Paper Thermo Fisher Scientific Cat#88600 Blotting-Grade Blocker BIO-RAD Cat#1706404 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34095 SuperSignal West Pico Plus Chemiluminescent Substrate Thermo Fisher Scientific Cat#34577 Monoclonal ANTI-FLAG M2Peroxidase (mouse) Sigma- Aldrich Cat# A8592, RRID:AB_439702 20% Arabinose KD Medical Cat#CAC-5020 Critical commercial assays Gibson Assembly Cloning Kit New England Biolabs Cat#E2621S Deposited data All original data and code produced in this work This paper https://zenodo.org/records/10672687 Original code produced in this study This paper https://github.com/IgorFesenko/ prokariotic_smORFs Accompanying interactive Colab Notebook This paper https://colab.research.google.com/github/ IgorFesenko/prokariotic_smORFs/blob/ main/ismORFs_resource.ipynb Software and algorithms CD-HIT Li and Godzik et al.103 https://github.com/weizhongli/cdhit RNAcode Washietl et al.33 https://github.com/ViennaRNA/RNAcode MEGA X Kumar et al.104 https://www.megasoftware.net/ MAFFT v7.475 Katoh and Standley105 https://mafft.cbrc.jp/alignment/software/ HH-Suite Steinegger et al.65 https://github.com/soedinglab/hh-suite orfipy Singh and Wurtele106 https://github.com/urmi-21/orfipy SmORFinder Durrant and Bhatt36 https://github.com/bhattlab/SmORFinder Biopython Cock et al.107 https://biopython.org/ IQ-Tree Nguyen et al.108 http://www.iqtree.org/ InterProscan 5.60–92.0 Quevillon et al.72 https://github.com/ebi-pf-team/ interproscan SibeliaZ Minkin and Medvedev44 https://github.com/medvedevgroup/ SibeliaZ SignalP 6 Teufel et al.109 https://github.com/fteufel/signalp-6.0/ blob/main/installation_instructions.md NCBI BLAST+ suite Altschul et al.110; Johnson et al.111 https://ftp.ncbi.nlm.nih.gov/blast/ executables/blast+/LATEST/ R The R Project for Statistical Computing https://cran.r-project.org/ Python Python Software Foundation https://www.python.org MMseqs2 Hauser et al.41 https://github.com/soedinglab/MMseqs2 uShuffle Jiang et al.112 https://github.com/guma44/ushuffle trimgalore 0.6.7 Krueger113 https://github.com/FelixKrueger/ TrimGalore bowtie 2-2.5.1 Langmead and Salzberg114 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml HISAT2 2.2.1 Kim et al.115 http://daehwankimlab.github.io/hisat2/ (Continued on next page) e2 Molecular Cell 85, 1–18.e1–e6, March 6, 2025 ..

    Produced:

    Article Title: The hidden bacterial microproteome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Escherichia coli strain MG1655 minil::cmR Nadim Majdalani NM400 E. coli K-12 F- l- ilvG- rfb-50 rph-1 Lab stock MG1655 E. coli MG1655 mini-l:cat N. Majdalani NM400 E. coli MG1655 ORF.34481-SPA::kan This study GSO1268 E. coli MG1655 ORF.34913-SPA::kan This study GSO1269 E. coli MG1655 ORF.89829-SPA::kan This study GSO1270 E. coli MG1655 ORF.24169-SPA::kan This study GSO1271 E. coli MG1655 ORF.60640-SPA::kan This study GSO1272 E. coli MG1655 ORF.27988-SPA::kan This study GSO1273 E. coli MG1655 ORF.50946-SPA::kan This study GSO1274 E. coli MG1655 ORF.40689-SPA::kan This study GSO1275 E. coli MG1655 ORF.35968-SPA::kan This study GSO1276 E. coli MG1655 ORF.63424-SPA::kan This study GSO1277 E. coli MG1655 ORF.78845-SPA::kan This study GSO1278 E. coli MG1655 ORF.18101-SPA::kan This study GSO1279 E. coli MG1655 ORF.92637-SPA::kan This study GSO1280 E. coli MG1655 ORF.59530-SPA::kan This study GSO1281 E. coli MG1655 ORF.8970-SPA::kan This study GSO1282 E. coli MG1655 ORF.3078-SPA::kan This study GSO1283 E. coli MG1655 ybhL-SPA::kan This study GSO1284 E. coli MG1655 ybhL-SPA::kan/pBAD24 This study GSO1285 E. coli MG1655 ybhL-SPA::kan/pBAD24 ORF.3078 This study GSO1286 Chemicals, peptides, and recombinant proteins Sodium Chloride Aventor Cat#7647-14-5 Bacto Tryptone Thermo Fisher Scientific Cat#211705 Bacto Yeast Extract Thermo Fisher Scientific Cat#2122750 Potassium Sulfate Sigma- Aldrich Cat#7778-80-5 Ammonium Sulfate Sigma- Aldrich Cat# 7783-20-2 Potassium Phosphate Monobasic Sigma- Aldrich Cat#7778-77-0 Casamino Acids Aventor Cat#97063-378 Glycerol Chem-Impex International Cat#30144 Vitamin B1 KD Medical Cat#CAC-5360 Tris Buffer pH 7.5 KD Medical Cat#RGF-3370 Potassium Chloride KD Medical Cat#CAC-5321 Tris Glycine SDS 10X KD Medical Cat#RGF-3390 10% SDS KD Medical Cat#RGF-3230 10 X Phosphate-Buffered Saline (PBS) Corning Cat#46-013-M Quick-Load Purple 1KB Plus DNA Ladder New England Biolabs Cat#NO550S Q5 High- Fidelity 2X Master Mix New England Biolabs Cat#MO492S Gel Loading Dye (6X) New England Biolabs Cat#B7024S Fisher BioReagents EZ-RUN Prestained Rec Protein Ladder Thermo Fisher Scientific Cat#BP3603-500 (Continued on next page) Molecular Cell 85, 1–18.e1–e6, March 6, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER 4-20% Mini-PROTEAN TGX Precast Protein Gel BIO-RAD Cat#4561096 Laemmli SDS sample buffer reducing (6X) Thermo Fisher Scientific Cat#J61337.AD Nitrocellulose membrane Filter paper Invitrogen Cat#LC2000 Western Blotting Filter Paper Thermo Fisher Scientific Cat#88600 Blotting-Grade Blocker BIO-RAD Cat#1706404 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34095 SuperSignal West Pico Plus Chemiluminescent Substrate Thermo Fisher Scientific Cat#34577 Monoclonal ANTI-FLAG M2Peroxidase (mouse) Sigma- Aldrich Cat# A8592, RRID:AB_439702 20% Arabinose KD Medical Cat#CAC-5020 Critical commercial assays Gibson Assembly Cloning Kit New England Biolabs Cat#E2621S Deposited data All original data and code produced in this work This paper https://zenodo.org/records/10672687 Original code produced in this study This paper https://github.com/IgorFesenko/ prokariotic_smORFs Accompanying interactive Colab Notebook This paper https://colab.research.google.com/github/ IgorFesenko/prokariotic_smORFs/blob/ main/ismORFs_resource.ipynb Software and algorithms CD-HIT Li and Godzik et al.103 https://github.com/weizhongli/cdhit RNAcode Washietl et al.33 https://github.com/ViennaRNA/RNAcode MEGA X Kumar et al.104 https://www.megasoftware.net/ MAFFT v7.475 Katoh and Standley105 https://mafft.cbrc.jp/alignment/software/ HH-Suite Steinegger et al.65 https://github.com/soedinglab/hh-suite orfipy Singh and Wurtele106 https://github.com/urmi-21/orfipy SmORFinder Durrant and Bhatt36 https://github.com/bhattlab/SmORFinder Biopython Cock et al.107 https://biopython.org/ IQ-Tree Nguyen et al.108 http://www.iqtree.org/ InterProscan 5.60–92.0 Quevillon et al.72 https://github.com/ebi-pf-team/ interproscan SibeliaZ Minkin and Medvedev44 https://github.com/medvedevgroup/ SibeliaZ SignalP 6 Teufel et al.109 https://github.com/fteufel/signalp-6.0/ blob/main/installation_instructions.md NCBI BLAST+ suite Altschul et al.110; Johnson et al.111 https://ftp.ncbi.nlm.nih.gov/blast/ executables/blast+/LATEST/ R The R Project for Statistical Computing https://cran.r-project.org/ Python Python Software Foundation https://www.python.org MMseqs2 Hauser et al.41 https://github.com/soedinglab/MMseqs2 uShuffle Jiang et al.112 https://github.com/guma44/ushuffle trimgalore 0.6.7 Krueger113 https://github.com/FelixKrueger/ TrimGalore bowtie 2-2.5.1 Langmead and Salzberg114 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml HISAT2 2.2.1 Kim et al.115 http://daehwankimlab.github.io/hisat2/ (Continued on next page) e2 Molecular Cell 85, 1–18.e1–e6, March 6, 2025 ..

    Software:

    Article Title: The hidden bacterial microproteome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Escherichia coli strain MG1655 minil::cmR Nadim Majdalani NM400 E. coli K-12 F- l- ilvG- rfb-50 rph-1 Lab stock MG1655 E. coli MG1655 mini-l:cat N. Majdalani NM400 E. coli MG1655 ORF.34481-SPA::kan This study GSO1268 E. coli MG1655 ORF.34913-SPA::kan This study GSO1269 E. coli MG1655 ORF.89829-SPA::kan This study GSO1270 E. coli MG1655 ORF.24169-SPA::kan This study GSO1271 E. coli MG1655 ORF.60640-SPA::kan This study GSO1272 E. coli MG1655 ORF.27988-SPA::kan This study GSO1273 E. coli MG1655 ORF.50946-SPA::kan This study GSO1274 E. coli MG1655 ORF.40689-SPA::kan This study GSO1275 E. coli MG1655 ORF.35968-SPA::kan This study GSO1276 E. coli MG1655 ORF.63424-SPA::kan This study GSO1277 E. coli MG1655 ORF.78845-SPA::kan This study GSO1278 E. coli MG1655 ORF.18101-SPA::kan This study GSO1279 E. coli MG1655 ORF.92637-SPA::kan This study GSO1280 E. coli MG1655 ORF.59530-SPA::kan This study GSO1281 E. coli MG1655 ORF.8970-SPA::kan This study GSO1282 E. coli MG1655 ORF.3078-SPA::kan This study GSO1283 E. coli MG1655 ybhL-SPA::kan This study GSO1284 E. coli MG1655 ybhL-SPA::kan/pBAD24 This study GSO1285 E. coli MG1655 ybhL-SPA::kan/pBAD24 ORF.3078 This study GSO1286 Chemicals, peptides, and recombinant proteins Sodium Chloride Aventor Cat#7647-14-5 Bacto Tryptone Thermo Fisher Scientific Cat#211705 Bacto Yeast Extract Thermo Fisher Scientific Cat#2122750 Potassium Sulfate Sigma- Aldrich Cat#7778-80-5 Ammonium Sulfate Sigma- Aldrich Cat# 7783-20-2 Potassium Phosphate Monobasic Sigma- Aldrich Cat#7778-77-0 Casamino Acids Aventor Cat#97063-378 Glycerol Chem-Impex International Cat#30144 Vitamin B1 KD Medical Cat#CAC-5360 Tris Buffer pH 7.5 KD Medical Cat#RGF-3370 Potassium Chloride KD Medical Cat#CAC-5321 Tris Glycine SDS 10X KD Medical Cat#RGF-3390 10% SDS KD Medical Cat#RGF-3230 10 X Phosphate-Buffered Saline (PBS) Corning Cat#46-013-M Quick-Load Purple 1KB Plus DNA Ladder New England Biolabs Cat#NO550S Q5 High- Fidelity 2X Master Mix New England Biolabs Cat#MO492S Gel Loading Dye (6X) New England Biolabs Cat#B7024S Fisher BioReagents EZ-RUN Prestained Rec Protein Ladder Thermo Fisher Scientific Cat#BP3603-500 (Continued on next page) Molecular Cell 85, 1–18.e1–e6, March 6, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER 4-20% Mini-PROTEAN TGX Precast Protein Gel BIO-RAD Cat#4561096 Laemmli SDS sample buffer reducing (6X) Thermo Fisher Scientific Cat#J61337.AD Nitrocellulose membrane Filter paper Invitrogen Cat#LC2000 Western Blotting Filter Paper Thermo Fisher Scientific Cat#88600 Blotting-Grade Blocker BIO-RAD Cat#1706404 SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific Cat#34095 SuperSignal West Pico Plus Chemiluminescent Substrate Thermo Fisher Scientific Cat#34577 Monoclonal ANTI-FLAG M2Peroxidase (mouse) Sigma- Aldrich Cat# A8592, RRID:AB_439702 20% Arabinose KD Medical Cat#CAC-5020 Critical commercial assays Gibson Assembly Cloning Kit New England Biolabs Cat#E2621S Deposited data All original data and code produced in this work This paper https://zenodo.org/records/10672687 Original code produced in this study This paper https://github.com/IgorFesenko/ prokariotic_smORFs Accompanying interactive Colab Notebook This paper https://colab.research.google.com/github/ IgorFesenko/prokariotic_smORFs/blob/ main/ismORFs_resource.ipynb Software and algorithms CD-HIT Li and Godzik et al.103 https://github.com/weizhongli/cdhit RNAcode Washietl et al.33 https://github.com/ViennaRNA/RNAcode MEGA X Kumar et al.104 https://www.megasoftware.net/ MAFFT v7.475 Katoh and Standley105 https://mafft.cbrc.jp/alignment/software/ HH-Suite Steinegger et al.65 https://github.com/soedinglab/hh-suite orfipy Singh and Wurtele106 https://github.com/urmi-21/orfipy SmORFinder Durrant and Bhatt36 https://github.com/bhattlab/SmORFinder Biopython Cock et al.107 https://biopython.org/ IQ-Tree Nguyen et al.108 http://www.iqtree.org/ InterProscan 5.60–92.0 Quevillon et al.72 https://github.com/ebi-pf-team/ interproscan SibeliaZ Minkin and Medvedev44 https://github.com/medvedevgroup/ SibeliaZ SignalP 6 Teufel et al.109 https://github.com/fteufel/signalp-6.0/ blob/main/installation_instructions.md NCBI BLAST+ suite Altschul et al.110; Johnson et al.111 https://ftp.ncbi.nlm.nih.gov/blast/ executables/blast+/LATEST/ R The R Project for Statistical Computing https://cran.r-project.org/ Python Python Software Foundation https://www.python.org MMseqs2 Hauser et al.41 https://github.com/soedinglab/MMseqs2 uShuffle Jiang et al.112 https://github.com/guma44/ushuffle trimgalore 0.6.7 Krueger113 https://github.com/FelixKrueger/ TrimGalore bowtie 2-2.5.1 Langmead and Salzberg114 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml HISAT2 2.2.1 Kim et al.115 http://daehwankimlab.github.io/hisat2/ (Continued on next page) e2 Molecular Cell 85, 1–18.e1–e6, March 6, 2025 ..

    Article Title: Quantitative 3D analysis and visualization of cardiac fibrosis by microcomputed tomography.
    Article Snippet: .. 1 Continued REAGENT or RESOURCE SOURCE IDENTIFIER 40% Acrylamide Bio-Rad Laboratories Cat# 1610140 2% Bis-acrylamide Bio-Rad Laboratories Cat# 1610142 VA044 NOVA Chemicals Cat# 017-19362 Saponin Sigma-Aldrich Cat# S4521 Paraformaldehyde (PFA) Sigma-Aldrich Cat# P6148 25% Glutaraldehyde Sigma-Aldrich Cat# G6257 Experimental models: Organisms/strains Mouse: Wild type [C57BL/6J] The Jackson Laboratory Stock No: 000664 Software and algorithms Skyscan1272 (v 1.1.19) Bruker Corporation https://www.bruker.com/products/ microtomography/micro-ctsoftware/3dsuite.html NRecon (v 1.7.1.0) Bruker Corporation Amira Software (v 2020.2) Thermo Fisher Scientific http://www.fei.com/software/amira3d-for-life-sciences/ RRID:SCR_007353 Other X-CLARITY Polymerization System Logos Biosystems Cat# C20001 SkyScan 1272 Bruker Corporation Cat# SkyScan1272 Orthodontic tray wax Kerr-Dental Cat# 09246 500 mL Bottle Top Vacuum Filter Corning Cat# CLS430513 Kimwipes (lint-free tissue paper) KIMTECH SCIENCE Cat# 34120 15 mL Falcon Corning Cat# 430791 ll OPEN ACCESS Protocol ..



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