Virus:Article Title: Rediversification following ecotype isolation reveals hidden adaptive potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Various LTEE-derived E. coli strains This paper See Table S1 Chemicals, peptides, and recombinant proteins RNAse-free DNAse Invitrogen Catalogue number: AM2222 Ready-Lyse Lysozyme Solution Lucigen Catalogue number: R1804M Critical commercial assays Monarch Total RNA Miniprep Kit New England BioLabs Catalogue number: T2010S Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Illumina Catalogue number: 20040529 DNeasy Blood and Tissue Kit Qiagen Catalogue number: 69504 NEBNext DNA Library Prep kit New England BioLabs Catalogue number: E7645 Nanopore ligation sequencing kit Oxford Nanopore Catalogue number: SQK-LSK109 Deposited data All DNA/RNA sequencing data This paper NCBI BioProject accession: PRJNA970313 REL606 genome Genbank NCBI RefSeq assembly: GCF_000017985.1 Processed data This paper https://github.com/joaoascensao/ Rediversification Oligonucleotides Oligonucleotides for genotyping and cloning This paper See Table S2 Recombinant DNA pBad-EBFP2 (plasmid with eBFP2 gene) Ai et al.89 Addgene catalog number: 14891 pMRE-Tn7-133 (miniTn7 plasmid to insert sYFP2 into genome at attTn7) Schlechter et al.90 Addgene catalog number: 118551 pJA17 (miniTn7 plasmid to insert eBFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; eBFP2 from pBad-EBFP2; BBa_J23119 promoter91; RBS designed in silico92 N/A pJA18 (miniTn7 plasmid to insert sYFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; BBa_J23119 promoter91; RBS designed in silico92 N/A Software and algorithms Code This paper https://github.com/joaoascensao/ Rediversification flowcytometrytools (v0.4.5) Yurtsev et al.93 https://eyurtsev.github.io/Flow CytometryTools/index.html minimap2 (v2.26) Li94 https://github.com/lh3/minimap2 Sniffles (v2.2) Sedlazeck et al.95 https://github.com/fritzsedlazeck/Sniffles HISAT2 (v2.2.0) Kim et al.96 https://daehwankimlab.github.io/hisat2/ featureCounts (v2.0.1) Liao et al.97 https://subread.sourceforge.net/ featureCounts.html DESeq2 (v1.38.3) Love et al.98 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html clusterProfiler (v4.6.2) Wu et al.99 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Other Attune Flow Cytometer (2017 model) ThermoFisher N/A (Continued on next page) e1 Current Biology 34, 855–867.e1–e6, February 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER SpectraMax 190 (shaking plate reader) Molecular Devices N/A Pippin Prep Sage Science N/A Femto pulse system Aligent N/A
Recombinant:Article Title: Rediversification following ecotype isolation reveals hidden adaptive potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Various LTEE-derived E. coli strains This paper See Table S1 Chemicals, peptides, and recombinant proteins RNAse-free DNAse Invitrogen Catalogue number: AM2222 Ready-Lyse Lysozyme Solution Lucigen Catalogue number: R1804M Critical commercial assays Monarch Total RNA Miniprep Kit New England BioLabs Catalogue number: T2010S Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Illumina Catalogue number: 20040529 DNeasy Blood and Tissue Kit Qiagen Catalogue number: 69504 NEBNext DNA Library Prep kit New England BioLabs Catalogue number: E7645 Nanopore ligation sequencing kit Oxford Nanopore Catalogue number: SQK-LSK109 Deposited data All DNA/RNA sequencing data This paper NCBI BioProject accession: PRJNA970313 REL606 genome Genbank NCBI RefSeq assembly: GCF_000017985.1 Processed data This paper https://github.com/joaoascensao/ Rediversification Oligonucleotides Oligonucleotides for genotyping and cloning This paper See Table S2 Recombinant DNA pBad-EBFP2 (plasmid with eBFP2 gene) Ai et al.89 Addgene catalog number: 14891 pMRE-Tn7-133 (miniTn7 plasmid to insert sYFP2 into genome at attTn7) Schlechter et al.90 Addgene catalog number: 118551 pJA17 (miniTn7 plasmid to insert eBFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; eBFP2 from pBad-EBFP2; BBa_J23119 promoter91; RBS designed in silico92 N/A pJA18 (miniTn7 plasmid to insert sYFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; BBa_J23119 promoter91; RBS designed in silico92 N/A Software and algorithms Code This paper https://github.com/joaoascensao/ Rediversification flowcytometrytools (v0.4.5) Yurtsev et al.93 https://eyurtsev.github.io/Flow CytometryTools/index.html minimap2 (v2.26) Li94 https://github.com/lh3/minimap2 Sniffles (v2.2) Sedlazeck et al.95 https://github.com/fritzsedlazeck/Sniffles HISAT2 (v2.2.0) Kim et al.96 https://daehwankimlab.github.io/hisat2/ featureCounts (v2.0.1) Liao et al.97 https://subread.sourceforge.net/ featureCounts.html DESeq2 (v1.38.3) Love et al.98 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html clusterProfiler (v4.6.2) Wu et al.99 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Other Attune Flow Cytometer (2017 model) ThermoFisher N/A (Continued on next page) e1 Current Biology 34, 855–867.e1–e6, February 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER SpectraMax 190 (shaking plate reader) Molecular Devices N/A Pippin Prep Sage Science N/A Femto pulse system Aligent N/A
Ligation:Article Title: Rediversification following ecotype isolation reveals hidden adaptive potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Various LTEE-derived E. coli strains This paper See Table S1 Chemicals, peptides, and recombinant proteins RNAse-free DNAse Invitrogen Catalogue number: AM2222 Ready-Lyse Lysozyme Solution Lucigen Catalogue number: R1804M Critical commercial assays Monarch Total RNA Miniprep Kit New England BioLabs Catalogue number: T2010S Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Illumina Catalogue number: 20040529 DNeasy Blood and Tissue Kit Qiagen Catalogue number: 69504 NEBNext DNA Library Prep kit New England BioLabs Catalogue number: E7645 Nanopore ligation sequencing kit Oxford Nanopore Catalogue number: SQK-LSK109 Deposited data All DNA/RNA sequencing data This paper NCBI BioProject accession: PRJNA970313 REL606 genome Genbank NCBI RefSeq assembly: GCF_000017985.1 Processed data This paper https://github.com/joaoascensao/ Rediversification Oligonucleotides Oligonucleotides for genotyping and cloning This paper See Table S2 Recombinant DNA pBad-EBFP2 (plasmid with eBFP2 gene) Ai et al.89 Addgene catalog number: 14891 pMRE-Tn7-133 (miniTn7 plasmid to insert sYFP2 into genome at attTn7) Schlechter et al.90 Addgene catalog number: 118551 pJA17 (miniTn7 plasmid to insert eBFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; eBFP2 from pBad-EBFP2; BBa_J23119 promoter91; RBS designed in silico92 N/A pJA18 (miniTn7 plasmid to insert sYFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; BBa_J23119 promoter91; RBS designed in silico92 N/A Software and algorithms Code This paper https://github.com/joaoascensao/ Rediversification flowcytometrytools (v0.4.5) Yurtsev et al.93 https://eyurtsev.github.io/Flow CytometryTools/index.html minimap2 (v2.26) Li94 https://github.com/lh3/minimap2 Sniffles (v2.2) Sedlazeck et al.95 https://github.com/fritzsedlazeck/Sniffles HISAT2 (v2.2.0) Kim et al.96 https://daehwankimlab.github.io/hisat2/ featureCounts (v2.0.1) Liao et al.97 https://subread.sourceforge.net/ featureCounts.html DESeq2 (v1.38.3) Love et al.98 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html clusterProfiler (v4.6.2) Wu et al.99 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Other Attune Flow Cytometer (2017 model) ThermoFisher N/A (Continued on next page) e1 Current Biology 34, 855–867.e1–e6, February 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER SpectraMax 190 (shaking plate reader) Molecular Devices N/A Pippin Prep Sage Science N/A Femto pulse system Aligent N/A
Sequencing:Article Title: Rediversification following ecotype isolation reveals hidden adaptive potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Various LTEE-derived E. coli strains This paper See Table S1 Chemicals, peptides, and recombinant proteins RNAse-free DNAse Invitrogen Catalogue number: AM2222 Ready-Lyse Lysozyme Solution Lucigen Catalogue number: R1804M Critical commercial assays Monarch Total RNA Miniprep Kit New England BioLabs Catalogue number: T2010S Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Illumina Catalogue number: 20040529 DNeasy Blood and Tissue Kit Qiagen Catalogue number: 69504 NEBNext DNA Library Prep kit New England BioLabs Catalogue number: E7645 Nanopore ligation sequencing kit Oxford Nanopore Catalogue number: SQK-LSK109 Deposited data All DNA/RNA sequencing data This paper NCBI BioProject accession: PRJNA970313 REL606 genome Genbank NCBI RefSeq assembly: GCF_000017985.1 Processed data This paper https://github.com/joaoascensao/ Rediversification Oligonucleotides Oligonucleotides for genotyping and cloning This paper See Table S2 Recombinant DNA pBad-EBFP2 (plasmid with eBFP2 gene) Ai et al.89 Addgene catalog number: 14891 pMRE-Tn7-133 (miniTn7 plasmid to insert sYFP2 into genome at attTn7) Schlechter et al.90 Addgene catalog number: 118551 pJA17 (miniTn7 plasmid to insert eBFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; eBFP2 from pBad-EBFP2; BBa_J23119 promoter91; RBS designed in silico92 N/A pJA18 (miniTn7 plasmid to insert sYFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; BBa_J23119 promoter91; RBS designed in silico92 N/A Software and algorithms Code This paper https://github.com/joaoascensao/ Rediversification flowcytometrytools (v0.4.5) Yurtsev et al.93 https://eyurtsev.github.io/Flow CytometryTools/index.html minimap2 (v2.26) Li94 https://github.com/lh3/minimap2 Sniffles (v2.2) Sedlazeck et al.95 https://github.com/fritzsedlazeck/Sniffles HISAT2 (v2.2.0) Kim et al.96 https://daehwankimlab.github.io/hisat2/ featureCounts (v2.0.1) Liao et al.97 https://subread.sourceforge.net/ featureCounts.html DESeq2 (v1.38.3) Love et al.98 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html clusterProfiler (v4.6.2) Wu et al.99 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Other Attune Flow Cytometer (2017 model) ThermoFisher N/A (Continued on next page) e1 Current Biology 34, 855–867.e1–e6, February 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER SpectraMax 190 (shaking plate reader) Molecular Devices N/A Pippin Prep Sage Science N/A Femto pulse system Aligent N/A
Cloning:Article Title: Rediversification following ecotype isolation reveals hidden adaptive potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Various LTEE-derived E. coli strains This paper See Table S1 Chemicals, peptides, and recombinant proteins RNAse-free DNAse Invitrogen Catalogue number: AM2222 Ready-Lyse Lysozyme Solution Lucigen Catalogue number: R1804M Critical commercial assays Monarch Total RNA Miniprep Kit New England BioLabs Catalogue number: T2010S Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Illumina Catalogue number: 20040529 DNeasy Blood and Tissue Kit Qiagen Catalogue number: 69504 NEBNext DNA Library Prep kit New England BioLabs Catalogue number: E7645 Nanopore ligation sequencing kit Oxford Nanopore Catalogue number: SQK-LSK109 Deposited data All DNA/RNA sequencing data This paper NCBI BioProject accession: PRJNA970313 REL606 genome Genbank NCBI RefSeq assembly: GCF_000017985.1 Processed data This paper https://github.com/joaoascensao/ Rediversification Oligonucleotides Oligonucleotides for genotyping and cloning This paper See Table S2 Recombinant DNA pBad-EBFP2 (plasmid with eBFP2 gene) Ai et al.89 Addgene catalog number: 14891 pMRE-Tn7-133 (miniTn7 plasmid to insert sYFP2 into genome at attTn7) Schlechter et al.90 Addgene catalog number: 118551 pJA17 (miniTn7 plasmid to insert eBFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; eBFP2 from pBad-EBFP2; BBa_J23119 promoter91; RBS designed in silico92 N/A pJA18 (miniTn7 plasmid to insert sYFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; BBa_J23119 promoter91; RBS designed in silico92 N/A Software and algorithms Code This paper https://github.com/joaoascensao/ Rediversification flowcytometrytools (v0.4.5) Yurtsev et al.93 https://eyurtsev.github.io/Flow CytometryTools/index.html minimap2 (v2.26) Li94 https://github.com/lh3/minimap2 Sniffles (v2.2) Sedlazeck et al.95 https://github.com/fritzsedlazeck/Sniffles HISAT2 (v2.2.0) Kim et al.96 https://daehwankimlab.github.io/hisat2/ featureCounts (v2.0.1) Liao et al.97 https://subread.sourceforge.net/ featureCounts.html DESeq2 (v1.38.3) Love et al.98 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html clusterProfiler (v4.6.2) Wu et al.99 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Other Attune Flow Cytometer (2017 model) ThermoFisher N/A (Continued on next page) e1 Current Biology 34, 855–867.e1–e6, February 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER SpectraMax 190 (shaking plate reader) Molecular Devices N/A Pippin Prep Sage Science N/A Femto pulse system Aligent N/A
Plasmid Preparation:Article Title: Rediversification following ecotype isolation reveals hidden adaptive potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Various LTEE-derived E. coli strains This paper See Table S1 Chemicals, peptides, and recombinant proteins RNAse-free DNAse Invitrogen Catalogue number: AM2222 Ready-Lyse Lysozyme Solution Lucigen Catalogue number: R1804M Critical commercial assays Monarch Total RNA Miniprep Kit New England BioLabs Catalogue number: T2010S Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Illumina Catalogue number: 20040529 DNeasy Blood and Tissue Kit Qiagen Catalogue number: 69504 NEBNext DNA Library Prep kit New England BioLabs Catalogue number: E7645 Nanopore ligation sequencing kit Oxford Nanopore Catalogue number: SQK-LSK109 Deposited data All DNA/RNA sequencing data This paper NCBI BioProject accession: PRJNA970313 REL606 genome Genbank NCBI RefSeq assembly: GCF_000017985.1 Processed data This paper https://github.com/joaoascensao/ Rediversification Oligonucleotides Oligonucleotides for genotyping and cloning This paper See Table S2 Recombinant DNA pBad-EBFP2 (plasmid with eBFP2 gene) Ai et al.89 Addgene catalog number: 14891 pMRE-Tn7-133 (miniTn7 plasmid to insert sYFP2 into genome at attTn7) Schlechter et al.90 Addgene catalog number: 118551 pJA17 (miniTn7 plasmid to insert eBFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; eBFP2 from pBad-EBFP2; BBa_J23119 promoter91; RBS designed in silico92 N/A pJA18 (miniTn7 plasmid to insert sYFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; BBa_J23119 promoter91; RBS designed in silico92 N/A Software and algorithms Code This paper https://github.com/joaoascensao/ Rediversification flowcytometrytools (v0.4.5) Yurtsev et al.93 https://eyurtsev.github.io/Flow CytometryTools/index.html minimap2 (v2.26) Li94 https://github.com/lh3/minimap2 Sniffles (v2.2) Sedlazeck et al.95 https://github.com/fritzsedlazeck/Sniffles HISAT2 (v2.2.0) Kim et al.96 https://daehwankimlab.github.io/hisat2/ featureCounts (v2.0.1) Liao et al.97 https://subread.sourceforge.net/ featureCounts.html DESeq2 (v1.38.3) Love et al.98 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html clusterProfiler (v4.6.2) Wu et al.99 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Other Attune Flow Cytometer (2017 model) ThermoFisher N/A (Continued on next page) e1 Current Biology 34, 855–867.e1–e6, February 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER SpectraMax 190 (shaking plate reader) Molecular Devices N/A Pippin Prep Sage Science N/A Femto pulse system Aligent N/A
Software:Article Title: Rediversification following ecotype isolation reveals hidden adaptive potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Various LTEE-derived E. coli strains This paper See Table S1 Chemicals, peptides, and recombinant proteins RNAse-free DNAse Invitrogen Catalogue number: AM2222 Ready-Lyse Lysozyme Solution Lucigen Catalogue number: R1804M Critical commercial assays Monarch Total RNA Miniprep Kit New England BioLabs Catalogue number: T2010S Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Illumina Catalogue number: 20040529 DNeasy Blood and Tissue Kit Qiagen Catalogue number: 69504 NEBNext DNA Library Prep kit New England BioLabs Catalogue number: E7645 Nanopore ligation sequencing kit Oxford Nanopore Catalogue number: SQK-LSK109 Deposited data All DNA/RNA sequencing data This paper NCBI BioProject accession: PRJNA970313 REL606 genome Genbank NCBI RefSeq assembly: GCF_000017985.1 Processed data This paper https://github.com/joaoascensao/ Rediversification Oligonucleotides Oligonucleotides for genotyping and cloning This paper See Table S2 Recombinant DNA pBad-EBFP2 (plasmid with eBFP2 gene) Ai et al.89 Addgene catalog number: 14891 pMRE-Tn7-133 (miniTn7 plasmid to insert sYFP2 into genome at attTn7) Schlechter et al.90 Addgene catalog number: 118551 pJA17 (miniTn7 plasmid to insert eBFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; eBFP2 from pBad-EBFP2; BBa_J23119 promoter91; RBS designed in silico92 N/A pJA18 (miniTn7 plasmid to insert sYFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; BBa_J23119 promoter91; RBS designed in silico92 N/A Software and algorithms Code This paper https://github.com/joaoascensao/ Rediversification flowcytometrytools (v0.4.5) Yurtsev et al.93 https://eyurtsev.github.io/Flow CytometryTools/index.html minimap2 (v2.26) Li94 https://github.com/lh3/minimap2 Sniffles (v2.2) Sedlazeck et al.95 https://github.com/fritzsedlazeck/Sniffles HISAT2 (v2.2.0) Kim et al.96 https://daehwankimlab.github.io/hisat2/ featureCounts (v2.0.1) Liao et al.97 https://subread.sourceforge.net/ featureCounts.html DESeq2 (v1.38.3) Love et al.98 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html clusterProfiler (v4.6.2) Wu et al.99 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Other Attune Flow Cytometer (2017 model) ThermoFisher N/A (Continued on next page) e1 Current Biology 34, 855–867.e1–e6, February 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER SpectraMax 190 (shaking plate reader) Molecular Devices N/A Pippin Prep Sage Science N/A Femto pulse system Aligent N/A
Flow Cytometry:Article Title: Rediversification following ecotype isolation reveals hidden adaptive potential.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Various LTEE-derived E. coli strains This paper See Table S1 Chemicals, peptides, and recombinant proteins RNAse-free DNAse Invitrogen Catalogue number: AM2222 Ready-Lyse Lysozyme Solution Lucigen Catalogue number: R1804M Critical commercial assays Monarch Total RNA Miniprep Kit New England BioLabs Catalogue number: T2010S Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Illumina Catalogue number: 20040529 DNeasy Blood and Tissue Kit Qiagen Catalogue number: 69504 NEBNext DNA Library Prep kit New England BioLabs Catalogue number: E7645 Nanopore ligation sequencing kit Oxford Nanopore Catalogue number: SQK-LSK109 Deposited data All DNA/RNA sequencing data This paper NCBI BioProject accession: PRJNA970313 REL606 genome Genbank NCBI RefSeq assembly: GCF_000017985.1 Processed data This paper https://github.com/joaoascensao/ Rediversification Oligonucleotides Oligonucleotides for genotyping and cloning This paper See Table S2 Recombinant DNA pBad-EBFP2 (plasmid with eBFP2 gene) Ai et al.89 Addgene catalog number: 14891 pMRE-Tn7-133 (miniTn7 plasmid to insert sYFP2 into genome at attTn7) Schlechter et al.90 Addgene catalog number: 118551 pJA17 (miniTn7 plasmid to insert eBFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; eBFP2 from pBad-EBFP2; BBa_J23119 promoter91; RBS designed in silico92 N/A pJA18 (miniTn7 plasmid to insert sYFP2 with strong promoter into genome at attTn7) Designed in this paper; Backbone from pMRE-Tn7-133; BBa_J23119 promoter91; RBS designed in silico92 N/A Software and algorithms Code This paper https://github.com/joaoascensao/ Rediversification flowcytometrytools (v0.4.5) Yurtsev et al.93 https://eyurtsev.github.io/Flow CytometryTools/index.html minimap2 (v2.26) Li94 https://github.com/lh3/minimap2 Sniffles (v2.2) Sedlazeck et al.95 https://github.com/fritzsedlazeck/Sniffles HISAT2 (v2.2.0) Kim et al.96 https://daehwankimlab.github.io/hisat2/ featureCounts (v2.0.1) Liao et al.97 https://subread.sourceforge.net/ featureCounts.html DESeq2 (v1.38.3) Love et al.98 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html clusterProfiler (v4.6.2) Wu et al.99 https://bioconductor.org/packages/ release/bioc/html/clusterProfiler.html Other Attune Flow Cytometer (2017 model) ThermoFisher N/A (Continued on next page) e1 Current Biology 34, 855–867.e1–e6, February 26, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER SpectraMax 190 (shaking plate reader) Molecular Devices N/A Pippin Prep Sage Science N/A Femto pulse system Aligent N/A
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