diff --git a/docs/_Experimental-Procedure-Standards-SOPs/DNA and RNA kits by sample b/docs/_Experimental-Procedure-Standards-SOPs/04-DNA-and-RNA-kits-by-sample.md similarity index 62% rename from docs/_Experimental-Procedure-Standards-SOPs/DNA and RNA kits by sample rename to docs/_Experimental-Procedure-Standards-SOPs/04-DNA-and-RNA-kits-by-sample.md index 8b707362..6a96c8d4 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/DNA and RNA kits by sample +++ b/docs/_Experimental-Procedure-Standards-SOPs/04-DNA-and-RNA-kits-by-sample.md @@ -1,62 +1,71 @@ -Nucleic Acid extraction kits +--- +title: DNA and RNA kits by sample +category: Experimental-Procedure-Standards-SOPs +layout: default +docs_css: markdown +--- -DNA extraction -Sponges - QIAamp® DNA Micro kit (QIAGEN)1 -Sponges –DNeasy® PowerSoil® Pro Kit (QIAGEN)1 -Human blood viruses - QIAAMP Ultra Sens Virus Kit (Qiagen)2 -Water samples - PowerSoil® DNA Isolation Kit (MoBio)3 -Saliva - QIAamp® DNA Mini kit (Qiagen)4 -Crushed fruit fly larvae - DNeasy PowerLyzer PowerSoil Kit-100 (Qiagen)5 -Frog skin swab – Prepman Ultra (ThermoFisher)6 -Skin swabs - PureLink® Genomic DNA Mini Kit (Life Technologies)7 -Skin swaps - Kaneka Easy DNA Extraction Kit version 2 (Kaneka Corp)8 -Oral swaps - QIAamp DNA mini kit (Qiagen)9 -Skin swaps - QIAamp blood and tissue DNA extraction kit (Qiagen)9 -Oyster haemolymph - Qiagen DNeasy Blood and Tissue Kit (Qiagen)10 -Molluscs - E.Z.N.A. Mollusc DNA (Omega Biotek)11 -Melted ice cave water - MoBio PowerWater DNA Isolation kit (MoBio)12 -BAL, oral rinse, tongue scraping, bronchoscope flush - DNeasy Blood and Tissue kit (Qiagen)13 -Lake sediment - PrestoTM Soil DNA Extraction Kit14 -Oral Swabs - Maxwell RSC PureFood Pathogen Kit (Promega)15 -Plant DNA - Mo Bio PowerSoil kit (Qiagen)16 -Gastric juice - DNeasy® PowerSoil Pro kit (Qiagen)17 -Saliva - DNeasy® PowerSoil Pro kit (Qiagen)18 -Bacterial DNA - DNeasy PowerSoil Kit (QIAGEN)19 -Soil - PowerSoil DNA Isolation Kit (Qiagen)20 -Soil - FastDNA Spin kit for soil (MP Bio)21 -Wastewater samples - Nucleo spin soil DNA kit (Macherey Nagel)22 -Saliva - OMNIgene ORAL OM-501 (Genotek)23 -Viral DNA - QIAGEN DNeasy Blood and Tissue Kit (Qiagen)24 -Viral DNA & RNA - AllPrep DNA/RNA Mini kit (Qiagen)25 -Microbial DNA - Mo Bio PowerSoil kit (Qiagen)25 -Phage DNA - QIAamp - DNA stool kit (Qiagen)26 -Bacterial & Viral DNA - Isolate II Genomic DNA Kit (Bioline)13 -Fungal DNA - Maxwell® RSC PureFood GMO and Authentication Kit (Promega)27 -Leaves - PureLink Genomic DNA (ThermoFisher)28 -Food – Power Food kit (Qiagen)33 -Mollusc tissues - Qiagen DNeasy Blood and Tissue Kit (Qiagen)34 JV -Yogurt - PowerSoil DNA Isolation Kit (MoBio)35 Pamela -Saliva - PowerSoil DNA Isolation Kit (MoBio)36, Pamela -Plasmid preparations: NucleoSpin Plasmid kit (Macherey-Nagel, Düren, DE)37 Maja -Bile samples - ZymoBIOMICS DNA/RNA Miniprep Kit38 NT -mouse small intestine content - ZymoBIOMICS DNA/RNA Miniprep Kit39 NT -Bacterial DNA from cultures (automated) - GenFind v3 Kit (Beckman Coulter)40 NT -Bacterial DNA from low biomass (eg. FACS sorted) samlpes – mericon DNA Bacteria Kit (Qiagen)41 NT -RNA extraction -Mosquitos - TRIzol LS (Invitrogen) – purified with RNeasy MinElute Cleanup Kit (Qiagen)29 -Sea Water - RNeasy mini kit (Qiagen)3 -Antarctic ticks - MagMax mirVana™ Total RNA isolation Kit (ThermoFisher Scientific)30 -Soil - PowerMax soil DNA isolation kit (Mo Bio)31 -Cervical samples - Smarter stranded total RNA-seq kit v2—pico input mammalian (Takara Bio)32 -Viral DNA & RNA - AllPrep DNA/RNA Mini kit (Qiagen)25 -Viral RNA - QIAmp Viral RNA kit (Qiagen)13 -Cerebellum, hippocampus and visual cortex - Uneasy Plus Universal Mini Kit (Qiagen)42 JV -Bile samples - ZymoBIOMICS DNA/RNA Miniprep Kit43 NT -mouse small intestine content - ZymoBIOMICS DNA/RNA Miniprep Kit44 NT +# Nucleic Acid extraction kits +## DNA extraction -References +- Sponges - QIAamp® DNA Micro kit (QIAGEN)1 +- Sponges –DNeasy® PowerSoil® Pro Kit (QIAGEN)1 +- Human blood viruses - QIAAMP Ultra Sens Virus Kit (Qiagen)2 +- Water samples - PowerSoil® DNA Isolation Kit (MoBio)3 +- Saliva - QIAamp® DNA Mini kit (Qiagen)4 +- Crushed fruit fly larvae - DNeasy PowerLyzer PowerSoil Kit-100 (Qiagen)5 +- Frog skin swab – Prepman Ultra (ThermoFisher)6 +- Skin swabs - PureLink® Genomic DNA Mini Kit (Life Technologies)7 +- Skin swaps - Kaneka Easy DNA Extraction Kit version 2 (Kaneka Corp)8 +- Oral swaps - QIAamp DNA mini kit (Qiagen)9 +- Skin swaps - QIAamp blood and tissue DNA extraction kit (Qiagen)9 +- Oyster haemolymph - Qiagen DNeasy Blood and Tissue Kit (Qiagen)10 +- Molluscs - E.Z.N.A. Mollusc DNA (Omega Biotek)11 +- Melted ice cave water - MoBio PowerWater DNA Isolation kit (MoBio)12 +- BAL, oral rinse, tongue scraping, bronchoscope flush - DNeasy Blood and Tissue kit (Qiagen)13 +- Lake sediment - PrestoTM Soil DNA Extraction Kit14 +- Oral Swabs - Maxwell RSC PureFood Pathogen Kit (Promega)15 +- Plant DNA - Mo Bio PowerSoil kit (Qiagen)16 +- Gastric juice - DNeasy® PowerSoil Pro kit (Qiagen)17 +- Saliva - DNeasy® PowerSoil Pro kit (Qiagen)18 +- Bacterial DNA - DNeasy PowerSoil Kit (QIAGEN)19 +- Soil - PowerSoil DNA Isolation Kit (Qiagen)20 +- Soil - FastDNA Spin kit for soil (MP Bio)21 +- Wastewater samples - Nucleo spin soil DNA kit (Macherey Nagel)22 +- Saliva - OMNIgene ORAL OM-501 (Genotek)23 +- Viral DNA - QIAGEN DNeasy Blood and Tissue Kit (Qiagen)24 +- Viral DNA & RNA - AllPrep DNA/RNA Mini kit (Qiagen)25 +- Microbial DNA - Mo Bio PowerSoil kit (Qiagen)25 +- Phage DNA - QIAamp - DNA stool kit (Qiagen)26 +- Bacterial & Viral DNA - Isolate II Genomic DNA Kit (Bioline)13 +- Fungal DNA - Maxwell® RSC PureFood GMO and Authentication Kit (Promega)27 +- Leaves - PureLink Genomic DNA (ThermoFisher)28 +- Food – Power Food kit (Qiagen)33 +- Mollusc tissues - Qiagen DNeasy Blood and Tissue Kit (Qiagen)34 JV +- Yogurt - PowerSoil DNA Isolation Kit (MoBio)35 Pamela +- Saliva - PowerSoil DNA Isolation Kit (MoBio)36, Pamela +- Plasmid preparations: NucleoSpin Plasmid kit (Macherey-Nagel, Düren, DE)37 Maja +- Bile samples - ZymoBIOMICS DNA/RNA Miniprep Kit38 NT +- mouse small intestine content - ZymoBIOMICS DNA/RNA Miniprep Kit39 NT +- Bacterial DNA from cultures (automated) - GenFind v3 Kit (Beckman Coulter)40 NT +- Bacterial DNA from low biomass (eg. FACS sorted) samlpes – mericon DNA Bacteria Kit (Qiagen)41 NT + +## RNA extraction +- Mosquitos - TRIzol LS (Invitrogen) – purified with RNeasy MinElute Cleanup Kit (Qiagen)29 +- Sea Water - RNeasy mini kit (Qiagen)3 +- Antarctic ticks - MagMax mirVana™ Total RNA isolation Kit (ThermoFisher Scientific)30 +- Soil - PowerMax soil DNA isolation kit (Mo Bio)31 +- Cervical samples - Smarter stranded total RNA-seq kit v2—pico input mammalian (Takara Bio)32 +- Viral DNA & RNA - AllPrep DNA/RNA Mini kit (Qiagen)25 +- Viral RNA - QIAmp Viral RNA kit (Qiagen)13 +- Cerebellum, hippocampus and visual cortex - Uneasy Plus Universal Mini Kit (Qiagen)42 JV +- Bile samples - ZymoBIOMICS DNA/RNA Miniprep Kit43 NT +- mouse small intestine content - ZymoBIOMICS DNA/RNA Miniprep Kit44 NT + + +##References 1. Ruocco, N. et al. Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis. Scientific Reports 2021 11:1 11, 1–12 (2021). 2. Cebriá-Mendoza, M. et al. Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans. Scientific Reports 2021 11:1 11, 1–11 (2021). 3. Martínez-Pérez, C. et al. Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf. Nature Communications 2022 13:1 13, 1–15 (2022). diff --git a/docs/_Experimental-Procedure-Standards-SOPs/Lipid and fatty acid extraction protocol from biological samples b/docs/_Experimental-Procedure-Standards-SOPs/05-Lipid-and-fatty-acid-extraction-protocol-from-biological-samples.md similarity index 95% rename from docs/_Experimental-Procedure-Standards-SOPs/Lipid and fatty acid extraction protocol from biological samples rename to docs/_Experimental-Procedure-Standards-SOPs/05-Lipid-and-fatty-acid-extraction-protocol-from-biological-samples.md index 5eb5a50f..0aed87a8 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/Lipid and fatty acid extraction protocol from biological samples +++ b/docs/_Experimental-Procedure-Standards-SOPs/05-Lipid-and-fatty-acid-extraction-protocol-from-biological-samples.md @@ -1,3 +1,10 @@ +--- +title: Lipid and fatty acid extraction protocol from biological samples +category: Experimental-Procedure-Standards-SOPs +layout: default +docs_css: markdown +--- + Protocol/MCF/SamplePrep/02: Lipid and fatty acid extraction protocol from biological samples Aim: Lipid extraction from mammalian cells or microbial samples for LC-MS analysis diff --git a/docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from adherent mammalian cells b/docs/_Experimental-Procedure-Standards-SOPs/06-Metabolite-extraction-from-adherent-mammalian-cells.md similarity index 93% rename from docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from adherent mammalian cells rename to docs/_Experimental-Procedure-Standards-SOPs/06-Metabolite-extraction-from-adherent-mammalian-cells.md index ad2ce127..e07a44f5 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from adherent mammalian cells +++ b/docs/_Experimental-Procedure-Standards-SOPs/06-Metabolite-extraction-from-adherent-mammalian-cells.md @@ -1,4 +1,11 @@ - Protocol/MCF/SamplePrep/01: Metabolite extraction from adherent mammalian cells +--- +title: Metabolite extraction from adherent mammalian cells +category: Experimental-Procedure-Standards-SOPs +layout: default +docs_css: markdown +--- + +Protocol/MCF/SamplePrep/01: Metabolite extraction from adherent mammalian cells Aim: Aqueous metabolite extraction from mammalian cells or microbial samples for LC-MS analysis diff --git a/docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from plant tissue b/docs/_Experimental-Procedure-Standards-SOPs/07-Metabolite-extraction-from-plant-tissue.md similarity index 94% rename from docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from plant tissue rename to docs/_Experimental-Procedure-Standards-SOPs/07-Metabolite-extraction-from-plant-tissue.md index b087d91b..05283d0d 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from plant tissue +++ b/docs/_Experimental-Procedure-Standards-SOPs/07-Metabolite-extraction-from-plant-tissue.md @@ -1,3 +1,11 @@ +--- +title: Metabolite extraction from plant tissue +category: Experimental-Procedure-Standards-SOPs +layout: default +docs_css: markdown +--- + + Protocol/MCF/SamplePrep/03: Metabolite extraction from plant tissues Sample required:Plant material required: 20-50 mg finely homogenized tissue diff --git a/docs/_Experimental-Procedure-Standards-SOPs/Proteomics - TMT-labelled SP3 method b/docs/_Experimental-Procedure-Standards-SOPs/08-Proteomics-TMT-labelled-SP3-method.md similarity index 97% rename from docs/_Experimental-Procedure-Standards-SOPs/Proteomics - TMT-labelled SP3 method rename to docs/_Experimental-Procedure-Standards-SOPs/08-Proteomics-TMT-labelled-SP3-method.md index d56953db..5277bac0 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/Proteomics - TMT-labelled SP3 method +++ b/docs/_Experimental-Procedure-Standards-SOPs/08-Proteomics-TMT-labelled-SP3-method.md @@ -1,3 +1,11 @@ +--- +title: Proteomics TMT labelled SP3 method +category: Experimental-Procedure-Standards-SOPs +layout: default +docs_css: markdown +--- + + TMT-labelled SP3 method Buffers: diff --git a/docs/_Experimental-Procedure-Standards-SOPs/Sample Collection and Storage by Sample b/docs/_Experimental-Procedure-Standards-SOPs/09-Sample-Collection-and-Storage-by-Sample.md similarity index 98% rename from docs/_Experimental-Procedure-Standards-SOPs/Sample Collection and Storage by Sample rename to docs/_Experimental-Procedure-Standards-SOPs/09-Sample-Collection-and-Storage-by-Sample.md index 2f4750be..1aebb9b6 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/Sample Collection and Storage by Sample +++ b/docs/_Experimental-Procedure-Standards-SOPs/09-Sample-Collection-and-Storage-by-Sample.md @@ -1,3 +1,10 @@ +--- +title: Sample Collection and Storage by Sample +category: Experimental-Procedure-Standards-SOPs +layout: default +docs_css: markdown +--- + General Protein Storage1 For short-term storage (~24h), most proteins can be kept at 4°C. For long-term storage, protein samples are typically kept at -20°C or -80°C. Protein storage at -20°C usually requires the addition of 50% glycerol to your sample to avoid freezing at this temperature. If we plan to store a protein at -20°C, we generally run the final size exclusion chromatography step in 2x storage buffer and then dilute the sample 1:1 with 100% glycerol. Alternatively, the protein sample can also be dialysed against the storage buffer already containing 50% glycerol. Proteins stored at -20ºC are often stable for several months, although the exact time frame is protein-dependent and should be determined experimentally.