diff --git a/.gitattributes b/.gitattributes index fdeb8343e32a54bf04b32f6d77dd278404e7ab38..6608dceea17c177cb4c0f97b8acc880c98ea42a1 100644 --- a/.gitattributes +++ b/.gitattributes @@ -3,3 +3,4 @@ _publication/pnas.2221508120.sapp.pdf filter=lfs diff=lfs merge=lfs -text _publication/dataverse_files/Table[[:space:]]S2.xlsx filter=lfs diff=lfs merge=lfs -text assays/Screen[[:space:]]for[[:space:]]antagonistic[[:space:]]interbacterial[[:space:]]interactions/dataset/Table[[:space:]]S2.xlsx filter=lfs diff=lfs merge=lfs -text +assays/BGC[[:space:]]prediction[[:space:]]using[[:space:]]antiSMASH/dataset/Table[[:space:]]S2.xlsx filter=lfs diff=lfs merge=lfs -text diff --git a/assays/MetabolomicAnalysis/README.md b/assays/BGC prediction using antiSMASH/README.md similarity index 100% rename from assays/MetabolomicAnalysis/README.md rename to assays/BGC prediction using antiSMASH/README.md diff --git a/assays/MetabolomicAnalysis/dataset/.gitkeep b/assays/BGC prediction using antiSMASH/dataset/.gitkeep similarity index 100% rename from assays/MetabolomicAnalysis/dataset/.gitkeep rename to assays/BGC prediction using antiSMASH/dataset/.gitkeep diff --git a/assays/BGC prediction using antiSMASH/dataset/Table S2.xlsx b/assays/BGC prediction using antiSMASH/dataset/Table S2.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..3efd1aa456ec24ff7e3c79fff6e7982cb2cc3f89 --- /dev/null +++ b/assays/BGC prediction using antiSMASH/dataset/Table S2.xlsx @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c069c9709aa2030dcebe88d4341730a998802c92b0d05874b6c0c8729fb9d3c0 +size 4062801 diff --git a/assays/BGC prediction using antiSMASH/isa.assay.xlsx b/assays/BGC prediction using antiSMASH/isa.assay.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..ed55e935edd00bcd0e4d46037b83f069d16afde8 Binary files /dev/null and b/assays/BGC prediction using antiSMASH/isa.assay.xlsx differ diff --git a/assays/MetabolomicAnalysis/protocols/.gitkeep b/assays/BGC prediction using antiSMASH/protocols/.gitkeep similarity index 100% rename from assays/MetabolomicAnalysis/protocols/.gitkeep rename to assays/BGC prediction using antiSMASH/protocols/.gitkeep diff --git a/assays/BGC prediction using antiSMASH/protocols/BGCAntiSMASH.md b/assays/BGC prediction using antiSMASH/protocols/BGCAntiSMASH.md new file mode 100644 index 0000000000000000000000000000000000000000..567d6544c8c0de852bef58d6ea7cf3ca58173bdf --- /dev/null +++ b/assays/BGC prediction using antiSMASH/protocols/BGCAntiSMASH.md @@ -0,0 +1,3 @@ +## BGC prediction using antiSMASH + +Bacterial genomes were downloaded from “www.at-sphere.com†or NCBI and https://antismash.secondarymetabolites.org/ version 6.0. Output data from antiSMASH analysis are listed as BGC classes and predicted BGCs for each genome in **Table S2**. Only high-quality genomes, as assessed by CheckM with ≥90% completeness and ≤5% contamination ratio were used for the analysis. For R401, the PacBio-sequenced high-quality genome was used for BGC prediction using antiSMASH. diff --git a/assays/DetectionOfR401DAPGandPyoverdine/isa.assay.xlsx b/assays/DetectionOfR401DAPGandPyoverdine/isa.assay.xlsx index 83487b87a3e8f49ae1100a8bc1d4c3397c6b73ef..d221ce145d147db2e80d4ed24475fa001840baf3 100644 Binary files a/assays/DetectionOfR401DAPGandPyoverdine/isa.assay.xlsx and b/assays/DetectionOfR401DAPGandPyoverdine/isa.assay.xlsx differ diff --git a/assays/Metabolomics Analysis/README.md b/assays/Metabolomics Analysis/README.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/Metabolomics Analysis/dataset/.gitkeep b/assays/Metabolomics Analysis/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/MetabolomicAnalysis/dataset/Metabolomics.md b/assays/Metabolomics Analysis/dataset/Metabolomics.md similarity index 100% rename from assays/MetabolomicAnalysis/dataset/Metabolomics.md rename to assays/Metabolomics Analysis/dataset/Metabolomics.md diff --git a/assays/MetabolomicAnalysis/isa.assay.xlsx b/assays/Metabolomics Analysis/isa.assay.xlsx similarity index 63% rename from assays/MetabolomicAnalysis/isa.assay.xlsx rename to assays/Metabolomics Analysis/isa.assay.xlsx index fde9a26ae419ad5beabc8193efba993c8c784dab..c5d7914de22a1e8be0feb3f7f57228bf32ae9cd8 100644 Binary files a/assays/MetabolomicAnalysis/isa.assay.xlsx and b/assays/Metabolomics Analysis/isa.assay.xlsx differ diff --git a/assays/Metabolomics Analysis/protocols/.gitkeep b/assays/Metabolomics Analysis/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/MetabolomicAnalysis/protocols/MetabolomicAnalysis.md b/assays/Metabolomics Analysis/protocols/MetabolomicAnalysis.md similarity index 100% rename from assays/MetabolomicAnalysis/protocols/MetabolomicAnalysis.md rename to assays/Metabolomics Analysis/protocols/MetabolomicAnalysis.md diff --git a/assays/Screen for antagonistic interbacterial interactions/isa.assay.xlsx b/assays/Screen for antagonistic interbacterial interactions/isa.assay.xlsx index 7b1eac32a44c5ac4a1db49f25ca84aa1e1c90859..6a295196d654f6892e0baeae865a72e6504fcebf 100644 Binary files a/assays/Screen for antagonistic interbacterial interactions/isa.assay.xlsx and b/assays/Screen for antagonistic interbacterial interactions/isa.assay.xlsx differ diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index 2a088ed43ac0fcf0a890e7ad6c02ebbf8b78ca1c..86ae0c4a13fcd1a7383820cd9a06606ceeb7774b 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/studies/Bacterial culture conditions/isa.study.xlsx b/studies/Bacterial culture conditions/isa.study.xlsx index 96ce5007ccd6dc34aa7aa4bac652723ef03e3027..8133fff8be918e6c123098044d41f0c372ece6db 100644 Binary files a/studies/Bacterial culture conditions/isa.study.xlsx and b/studies/Bacterial culture conditions/isa.study.xlsx differ diff --git a/studies/Plant Growth Conditions/isa.study.xlsx b/studies/Plant Growth Conditions/isa.study.xlsx index 893340bebb6e28a606e2c5b1a66bcf80d82e49db..4ae933e454ea6eda4b8c0ffa618c2175619a86c4 100644 Binary files a/studies/Plant Growth Conditions/isa.study.xlsx and b/studies/Plant Growth Conditions/isa.study.xlsx differ