From 5355d3d9070294c8340b40affe28e4ce480966f1 Mon Sep 17 00:00:00 2001
From: Viktoria Petrova <vipet103@hhu.de>
Date: Tue, 21 Nov 2023 13:56:38 +0200
Subject: [PATCH] change file names to Pascal case format
---
.../README.md | 0
.../dataset/.gitkeep | 0
.../isa.assay.xlsx | Bin
.../protocols/.gitkeep | 0
.../AbsorptionSpectraAndODMeasurements.md} | 0
.../README.md | 0
.../dataset/.gitkeep | 0
.../isa.assay.xlsx | Bin
.../protocols/.gitkeep | 0
.../protocols/DCWMeasurement.md} | 0
.../README.md | 0
.../dataset/.gitkeep | 0
.../isa.assay.xlsx | Bin
.../protocols/.gitkeep | 0
...urementsForTheQuantificationOfSqualene.md} | 0
.../README.md | 0
.../dataset/.gitkeep | 0
.../dataset/TableS6.XLSX | Bin
.../dataset/TableS7.XLSX | Bin
.../isa.assay.xlsx | Bin
.../protocols/.gitkeep | 0
...heIdentificationOfAmplificationTargets.md} | 0
.../protocols/TableS5.XLSX | Bin
.../README.md | 0
.../dataset/.gitkeep | 0
.../dataset/fpls-14-1024981-g003.jpg | Bin
.../isa.assay.xlsx | Bin
.../protocols/.gitkeep | 0
.../protocols/PigmentQuantification.md} | 0
.../isa.assay.xlsx | Bin 6797 -> 0 bytes
.../Quantitative real-time PCR (qRT-PCR).md | 2 --
.../README.md | 0
.../dataset/.gitkeep | 0
.../isa.assay.xlsx | Bin
.../protocols/.gitkeep | 0
.../Quantitative real-time PCR (qRT-PCR).md | 0
isa.investigation.xlsx | Bin 10428 -> 10451 bytes
.../README.md | 0
.../isa.study.xlsx | Bin 7441 -> 7452 bytes
.../protocols}/.gitkeep | 0
.../QuantificationOfSqualeneProduction.md} | 0
.../resources}/.gitkeep | 0
.../Plasmid and strain construction/README.md | 0
.../protocols/.gitkeep | 0
.../resources/.gitkeep | 0
.../README.md | 0
.../isa.study.xlsx | Bin 7403 -> 7414 bytes
.../protocols/.gitkeep | 0
.../protocols/PlasmidConstruction.md} | 0
.../protocols/PromoterInduction.md} | 0
.../protocols/StrainConstruction.md} | 0
.../resources/.gitkeep | 0
studies/Synechocystis/isa.study.xlsx | Bin 7538 -> 7538 bytes
...ure conditions.md => CultureConditions.md} | 0
54 files changed, 2 deletions(-)
rename assays/{Absorption spectra and OD measurements => AbsorptionSpectraAndODMeasurements}/README.md (100%)
rename assays/{Absorption spectra and OD measurements => AbsorptionSpectraAndODMeasurements}/dataset/.gitkeep (100%)
rename assays/{Absorption spectra and OD measurements => AbsorptionSpectraAndODMeasurements}/isa.assay.xlsx (100%)
rename assays/{Absorption spectra and OD measurements => AbsorptionSpectraAndODMeasurements}/protocols/.gitkeep (100%)
rename assays/{Absorption spectra and OD measurements/protocols/Absorption spectra and OD measurements.md => AbsorptionSpectraAndODMeasurements/protocols/AbsorptionSpectraAndODMeasurements.md} (100%)
rename assays/{DCW measurement => DCWMeasurement}/README.md (100%)
rename assays/{DCW measurement => DCWMeasurement}/dataset/.gitkeep (100%)
rename assays/{DCW measurement => DCWMeasurement}/isa.assay.xlsx (100%)
rename assays/{DCW measurement => DCWMeasurement}/protocols/.gitkeep (100%)
rename assays/{DCW measurement/protocols/DCW measurement.md => DCWMeasurement/protocols/DCWMeasurement.md} (100%)
rename assays/{GC-MS measurements for the quantification of squalene => GC-MSMeasurementsForTheQuantificationOfSqualene}/README.md (100%)
rename assays/{GC-MS measurements for the quantification of squalene => GC-MSMeasurementsForTheQuantificationOfSqualene}/dataset/.gitkeep (100%)
rename assays/{GC-MS measurements for the quantification of squalene => GC-MSMeasurementsForTheQuantificationOfSqualene}/isa.assay.xlsx (100%)
rename assays/{GC-MS measurements for the quantification of squalene => GC-MSMeasurementsForTheQuantificationOfSqualene}/protocols/.gitkeep (100%)
rename assays/{GC-MS measurements for the quantification of squalene/protocols/GC-MS measurements for the quantification of squalene.md => GC-MSMeasurementsForTheQuantificationOfSqualene/protocols/GC-MSMeasurementsForTheQuantificationOfSqualene.md} (100%)
rename assays/{Quantitative real-time PCR => MetabolicModeling}/README.md (100%)
rename assays/{Pigment quantification => MetabolicModeling}/dataset/.gitkeep (100%)
rename assays/{metabolic modeling => MetabolicModeling}/dataset/TableS6.XLSX (100%)
rename assays/{metabolic modeling => MetabolicModeling}/dataset/TableS7.XLSX (100%)
rename assays/{metabolic modeling => MetabolicModeling}/isa.assay.xlsx (100%)
rename assays/{Pigment quantification => MetabolicModeling}/protocols/.gitkeep (100%)
rename assays/{metabolic modeling/protocols/Metabolic modeling for the identification of amplification targets.md => MetabolicModeling/protocols/MetabolicModelingForTheIdentificationOfAmplificationTargets.md} (100%)
rename assays/{metabolic modeling => MetabolicModeling}/protocols/TableS5.XLSX (100%)
rename assays/{Pigment quantification => PigmentQuantification}/README.md (100%)
rename assays/{Quantitative real-time PCR => PigmentQuantification}/dataset/.gitkeep (100%)
rename assays/{Pigment quantification => PigmentQuantification}/dataset/fpls-14-1024981-g003.jpg (100%)
rename assays/{Pigment quantification => PigmentQuantification}/isa.assay.xlsx (100%)
rename assays/{Quantitative real-time PCR => PigmentQuantification}/protocols/.gitkeep (100%)
rename assays/{Pigment quantification/protocols/Pigment quantification.md => PigmentQuantification/protocols/PigmentQuantification.md} (100%)
delete mode 100644 assays/measurements and quantification/isa.assay.xlsx
delete mode 100644 assays/measurements and quantification/protocols/Quantitative real-time PCR (qRT-PCR).md
rename assays/{measurements and quantification => qPCR}/README.md (100%)
rename assays/{measurements and quantification => qPCR}/dataset/.gitkeep (100%)
rename assays/{Quantitative real-time PCR => qPCR}/isa.assay.xlsx (100%)
rename assays/{measurements and quantification => qPCR}/protocols/.gitkeep (100%)
rename assays/{Quantitative real-time PCR => qPCR}/protocols/Quantitative real-time PCR (qRT-PCR).md (100%)
rename {assays/metabolic modeling => studies/MeasurementsOfSqualeneProduction}/README.md (100%)
rename studies/{Measurements of squalene production => MeasurementsOfSqualeneProduction}/isa.study.xlsx (50%)
rename {assays/metabolic modeling/dataset => studies/MeasurementsOfSqualeneProduction/protocols}/.gitkeep (100%)
rename studies/{Measurements of squalene production/protocols/Quantification of squalene production.md => MeasurementsOfSqualeneProduction/protocols/QuantificationOfSqualeneProduction.md} (100%)
rename {assays/metabolic modeling/protocols => studies/MeasurementsOfSqualeneProduction/resources}/.gitkeep (100%)
delete mode 100644 studies/Plasmid and strain construction/README.md
delete mode 100644 studies/Plasmid and strain construction/protocols/.gitkeep
delete mode 100644 studies/Plasmid and strain construction/resources/.gitkeep
rename studies/{Measurements of squalene production => PlasmidAndStrainConstruction}/README.md (100%)
rename studies/{Plasmid and strain construction => PlasmidAndStrainConstruction}/isa.study.xlsx (50%)
rename studies/{Measurements of squalene production => PlasmidAndStrainConstruction}/protocols/.gitkeep (100%)
rename studies/{Plasmid and strain construction/protocols/Plasmid construction.md => PlasmidAndStrainConstruction/protocols/PlasmidConstruction.md} (100%)
rename studies/{Plasmid and strain construction/protocols/Promoter induction.md => PlasmidAndStrainConstruction/protocols/PromoterInduction.md} (100%)
rename studies/{Plasmid and strain construction/protocols/Strain construction.md => PlasmidAndStrainConstruction/protocols/StrainConstruction.md} (100%)
rename studies/{Measurements of squalene production => PlasmidAndStrainConstruction}/resources/.gitkeep (100%)
rename studies/Synechocystis/protocols/{Culture conditions.md => CultureConditions.md} (100%)
diff --git a/assays/Absorption spectra and OD measurements/README.md b/assays/AbsorptionSpectraAndODMeasurements/README.md
similarity index 100%
rename from assays/Absorption spectra and OD measurements/README.md
rename to assays/AbsorptionSpectraAndODMeasurements/README.md
diff --git a/assays/Absorption spectra and OD measurements/dataset/.gitkeep b/assays/AbsorptionSpectraAndODMeasurements/dataset/.gitkeep
similarity index 100%
rename from assays/Absorption spectra and OD measurements/dataset/.gitkeep
rename to assays/AbsorptionSpectraAndODMeasurements/dataset/.gitkeep
diff --git a/assays/Absorption spectra and OD measurements/isa.assay.xlsx b/assays/AbsorptionSpectraAndODMeasurements/isa.assay.xlsx
similarity index 100%
rename from assays/Absorption spectra and OD measurements/isa.assay.xlsx
rename to assays/AbsorptionSpectraAndODMeasurements/isa.assay.xlsx
diff --git a/assays/Absorption spectra and OD measurements/protocols/.gitkeep b/assays/AbsorptionSpectraAndODMeasurements/protocols/.gitkeep
similarity index 100%
rename from assays/Absorption spectra and OD measurements/protocols/.gitkeep
rename to assays/AbsorptionSpectraAndODMeasurements/protocols/.gitkeep
diff --git a/assays/Absorption spectra and OD measurements/protocols/Absorption spectra and OD measurements.md b/assays/AbsorptionSpectraAndODMeasurements/protocols/AbsorptionSpectraAndODMeasurements.md
similarity index 100%
rename from assays/Absorption spectra and OD measurements/protocols/Absorption spectra and OD measurements.md
rename to assays/AbsorptionSpectraAndODMeasurements/protocols/AbsorptionSpectraAndODMeasurements.md
diff --git a/assays/DCW measurement/README.md b/assays/DCWMeasurement/README.md
similarity index 100%
rename from assays/DCW measurement/README.md
rename to assays/DCWMeasurement/README.md
diff --git a/assays/DCW measurement/dataset/.gitkeep b/assays/DCWMeasurement/dataset/.gitkeep
similarity index 100%
rename from assays/DCW measurement/dataset/.gitkeep
rename to assays/DCWMeasurement/dataset/.gitkeep
diff --git a/assays/DCW measurement/isa.assay.xlsx b/assays/DCWMeasurement/isa.assay.xlsx
similarity index 100%
rename from assays/DCW measurement/isa.assay.xlsx
rename to assays/DCWMeasurement/isa.assay.xlsx
diff --git a/assays/DCW measurement/protocols/.gitkeep b/assays/DCWMeasurement/protocols/.gitkeep
similarity index 100%
rename from assays/DCW measurement/protocols/.gitkeep
rename to assays/DCWMeasurement/protocols/.gitkeep
diff --git a/assays/DCW measurement/protocols/DCW measurement.md b/assays/DCWMeasurement/protocols/DCWMeasurement.md
similarity index 100%
rename from assays/DCW measurement/protocols/DCW measurement.md
rename to assays/DCWMeasurement/protocols/DCWMeasurement.md
diff --git a/assays/GC-MS measurements for the quantification of squalene/README.md b/assays/GC-MSMeasurementsForTheQuantificationOfSqualene/README.md
similarity index 100%
rename from assays/GC-MS measurements for the quantification of squalene/README.md
rename to assays/GC-MSMeasurementsForTheQuantificationOfSqualene/README.md
diff --git a/assays/GC-MS measurements for the quantification of squalene/dataset/.gitkeep b/assays/GC-MSMeasurementsForTheQuantificationOfSqualene/dataset/.gitkeep
similarity index 100%
rename from assays/GC-MS measurements for the quantification of squalene/dataset/.gitkeep
rename to assays/GC-MSMeasurementsForTheQuantificationOfSqualene/dataset/.gitkeep
diff --git a/assays/GC-MS measurements for the quantification of squalene/isa.assay.xlsx b/assays/GC-MSMeasurementsForTheQuantificationOfSqualene/isa.assay.xlsx
similarity index 100%
rename from assays/GC-MS measurements for the quantification of squalene/isa.assay.xlsx
rename to assays/GC-MSMeasurementsForTheQuantificationOfSqualene/isa.assay.xlsx
diff --git a/assays/GC-MS measurements for the quantification of squalene/protocols/.gitkeep b/assays/GC-MSMeasurementsForTheQuantificationOfSqualene/protocols/.gitkeep
similarity index 100%
rename from assays/GC-MS measurements for the quantification of squalene/protocols/.gitkeep
rename to assays/GC-MSMeasurementsForTheQuantificationOfSqualene/protocols/.gitkeep
diff --git a/assays/GC-MS measurements for the quantification of squalene/protocols/GC-MS measurements for the quantification of squalene.md b/assays/GC-MSMeasurementsForTheQuantificationOfSqualene/protocols/GC-MSMeasurementsForTheQuantificationOfSqualene.md
similarity index 100%
rename from assays/GC-MS measurements for the quantification of squalene/protocols/GC-MS measurements for the quantification of squalene.md
rename to assays/GC-MSMeasurementsForTheQuantificationOfSqualene/protocols/GC-MSMeasurementsForTheQuantificationOfSqualene.md
diff --git a/assays/Quantitative real-time PCR/README.md b/assays/MetabolicModeling/README.md
similarity index 100%
rename from assays/Quantitative real-time PCR/README.md
rename to assays/MetabolicModeling/README.md
diff --git a/assays/Pigment quantification/dataset/.gitkeep b/assays/MetabolicModeling/dataset/.gitkeep
similarity index 100%
rename from assays/Pigment quantification/dataset/.gitkeep
rename to assays/MetabolicModeling/dataset/.gitkeep
diff --git a/assays/metabolic modeling/dataset/TableS6.XLSX b/assays/MetabolicModeling/dataset/TableS6.XLSX
similarity index 100%
rename from assays/metabolic modeling/dataset/TableS6.XLSX
rename to assays/MetabolicModeling/dataset/TableS6.XLSX
diff --git a/assays/metabolic modeling/dataset/TableS7.XLSX b/assays/MetabolicModeling/dataset/TableS7.XLSX
similarity index 100%
rename from assays/metabolic modeling/dataset/TableS7.XLSX
rename to assays/MetabolicModeling/dataset/TableS7.XLSX
diff --git a/assays/metabolic modeling/isa.assay.xlsx b/assays/MetabolicModeling/isa.assay.xlsx
similarity index 100%
rename from assays/metabolic modeling/isa.assay.xlsx
rename to assays/MetabolicModeling/isa.assay.xlsx
diff --git a/assays/Pigment quantification/protocols/.gitkeep b/assays/MetabolicModeling/protocols/.gitkeep
similarity index 100%
rename from assays/Pigment quantification/protocols/.gitkeep
rename to assays/MetabolicModeling/protocols/.gitkeep
diff --git a/assays/metabolic modeling/protocols/Metabolic modeling for the identification of amplification targets.md b/assays/MetabolicModeling/protocols/MetabolicModelingForTheIdentificationOfAmplificationTargets.md
similarity index 100%
rename from assays/metabolic modeling/protocols/Metabolic modeling for the identification of amplification targets.md
rename to assays/MetabolicModeling/protocols/MetabolicModelingForTheIdentificationOfAmplificationTargets.md
diff --git a/assays/metabolic modeling/protocols/TableS5.XLSX b/assays/MetabolicModeling/protocols/TableS5.XLSX
similarity index 100%
rename from assays/metabolic modeling/protocols/TableS5.XLSX
rename to assays/MetabolicModeling/protocols/TableS5.XLSX
diff --git a/assays/Pigment quantification/README.md b/assays/PigmentQuantification/README.md
similarity index 100%
rename from assays/Pigment quantification/README.md
rename to assays/PigmentQuantification/README.md
diff --git a/assays/Quantitative real-time PCR/dataset/.gitkeep b/assays/PigmentQuantification/dataset/.gitkeep
similarity index 100%
rename from assays/Quantitative real-time PCR/dataset/.gitkeep
rename to assays/PigmentQuantification/dataset/.gitkeep
diff --git a/assays/Pigment quantification/dataset/fpls-14-1024981-g003.jpg b/assays/PigmentQuantification/dataset/fpls-14-1024981-g003.jpg
similarity index 100%
rename from assays/Pigment quantification/dataset/fpls-14-1024981-g003.jpg
rename to assays/PigmentQuantification/dataset/fpls-14-1024981-g003.jpg
diff --git a/assays/Pigment quantification/isa.assay.xlsx b/assays/PigmentQuantification/isa.assay.xlsx
similarity index 100%
rename from assays/Pigment quantification/isa.assay.xlsx
rename to assays/PigmentQuantification/isa.assay.xlsx
diff --git a/assays/Quantitative real-time PCR/protocols/.gitkeep b/assays/PigmentQuantification/protocols/.gitkeep
similarity index 100%
rename from assays/Quantitative real-time PCR/protocols/.gitkeep
rename to assays/PigmentQuantification/protocols/.gitkeep
diff --git a/assays/Pigment quantification/protocols/Pigment quantification.md b/assays/PigmentQuantification/protocols/PigmentQuantification.md
similarity index 100%
rename from assays/Pigment quantification/protocols/Pigment quantification.md
rename to assays/PigmentQuantification/protocols/PigmentQuantification.md
diff --git a/assays/measurements and quantification/isa.assay.xlsx b/assays/measurements and quantification/isa.assay.xlsx
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diff --git a/assays/measurements and quantification/protocols/Quantitative real-time PCR (qRT-PCR).md b/assays/measurements and quantification/protocols/Quantitative real-time PCR (qRT-PCR).md
deleted file mode 100644
index 886784a..0000000
--- a/assays/measurements and quantification/protocols/Quantitative real-time PCR (qRT-PCR).md
+++ /dev/null
@@ -1,2 +0,0 @@
-## Quantitative real-time PCR (qRT-PCR)
-Cultures were sampled (0.5 ml) after 72 hours at the end of the growth experiment. The pellet was processed for RNA extraction using the PGTX method (dx.doi.org/10.17504/protocols.io.jm3ck8n, Pinto et al., 2009). The remaining DNA in the extracted RNA was removed by DNase digestion using the TURBO DNA-free™ (ThermoFischer) kit according to the manufacturer’s instructions. Extracted RNAs (250 ng) were used in a reverse transcriptase reaction using the RevertAid First Strand cDNA Synthesis Kit (ThermoFischer) according to the manufacturer’s instructions. The resulting cDNA was diluted 1:20. For performing qPCR, the DyNAmo ColorFlash SYBR Green qPCR Kit was used according to the manufacturer’s instructions. Primers for sqs, dxs and the housekeeping gene rpoA are shown in Table S2 (SI). Primer efficiencies were tested before performing qRT-PCR and were deemed sufficient to yield quantitative information (Figure S3; Table S3 (SI)). Changes in gene expression as fold changes compared to the control were determined using the 2−ΔΔCT method, using rpoA as a housekeeping gene and the Δshc strain subjected to the same rhamnose concentration as a control.
\ No newline at end of file
diff --git a/assays/measurements and quantification/README.md b/assays/qPCR/README.md
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diff --git a/assays/measurements and quantification/dataset/.gitkeep b/assays/qPCR/dataset/.gitkeep
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diff --git a/assays/Quantitative real-time PCR/isa.assay.xlsx b/assays/qPCR/isa.assay.xlsx
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rename from assays/Quantitative real-time PCR/isa.assay.xlsx
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diff --git a/assays/measurements and quantification/protocols/.gitkeep b/assays/qPCR/protocols/.gitkeep
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diff --git a/assays/Quantitative real-time PCR/protocols/Quantitative real-time PCR (qRT-PCR).md b/assays/qPCR/protocols/Quantitative real-time PCR (qRT-PCR).md
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rename to assays/qPCR/protocols/Quantitative real-time PCR (qRT-PCR).md
diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
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diff --git a/assays/metabolic modeling/README.md b/studies/MeasurementsOfSqualeneProduction/README.md
similarity index 100%
rename from assays/metabolic modeling/README.md
rename to studies/MeasurementsOfSqualeneProduction/README.md
diff --git a/studies/Measurements of squalene production/isa.study.xlsx b/studies/MeasurementsOfSqualeneProduction/isa.study.xlsx
similarity index 50%
rename from studies/Measurements of squalene production/isa.study.xlsx
rename to studies/MeasurementsOfSqualeneProduction/isa.study.xlsx
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