From 2792f972060fc197bf8fd5c7920b1874ac32bbbd Mon Sep 17 00:00:00 2001
From: saschulz <105273410+saschulz@users.noreply.github.com>
Date: Wed, 11 Oct 2023 16:22:53 +0200
Subject: [PATCH 1/7] Create Proteomics - TMT-labelled SP3 method

added SOP
---
 .../Proteomics - TMT-labelled SP3 method      | 97 +++++++++++++++++++
 1 file changed, 97 insertions(+)
 create mode 100644 docs/_Experimental-Procedure-Standards-SOPs/Proteomics - TMT-labelled SP3 method

diff --git a/docs/_Experimental-Procedure-Standards-SOPs/Proteomics - TMT-labelled SP3 method b/docs/_Experimental-Procedure-Standards-SOPs/Proteomics - TMT-labelled SP3 method
new file mode 100644
index 00000000..d56953db
--- /dev/null
+++ b/docs/_Experimental-Procedure-Standards-SOPs/Proteomics - TMT-labelled SP3 method	
@@ -0,0 +1,97 @@
+TMT-labelled SP3 method
+
+Buffers:
+NP40-Lysis buffer
+898.5 µl PBS
+80 µl 10% NP-40 in PBS
+1.5 ul 1M MgCl2
+20 µl 50x protease inhibitor cocktail EDTA-free
+
+Plate wash buffer
+920 µl PBS
+80 µl 10% NP-40 in PBS
+
+DTT (reducing buffer)
+200 mM dithiothreitol (DTT) in 50 mM HEPES/NaOH, pH 8.5 or Milli Q (add 500 µl)
+
+CAA (alkylating buffer)
+400 mM 2-chloroacetamide (CAA) in 50 mM HEPES/NaOH pH 8.5 or Milli Q (add 500 µl)
+
+Cell Lysis and Protein Preparation
+1. Add 100 µl of ice cold NP40-Lysis buffer to a cell pellet of 1*106 HEK293T cells and resuspend the cell pellet by pipetting up and down. 
+2. Sample A: transfer 36 µl to 1.5 ml Eppendorf tube and add 1.5 µl of benzonase. Incubate sample on ice until Sample B is prepared. 
+3. Sample B: Equilibrate a 0.45 µm filter plate with 50 µl plate wash buffer. Place filter plate on 96well plate and spin down for 2 min at 1.200 rpm at 4 °C. Place filter plate on new 96well plate and transfer the remaining NP40 lysate to the equilibrated filter plate. Centrifuge (500 g, 10 min, 4°C). Transfer 36 µl of the filtrate to a 1.5 ml Eppendorf tube. Add 1.5 µl benzonase and incubate sample for 5 min on ice. 
+4. Add 2 µl of 20% SDS to Sample A and B and incubate both lysates for 10 min at 37°C while shaking. 
+5. Add 2 µL of 200 mM DTT (10 mM final concentration) and incubate for 20 minutes at 45°C. 
+6. Add 2 µL of 400 mM CAA (20 mM final concentration) and incubate for 20 minutes at 24°C. 
+7. Add 1 µL of 200 mM DTT to quench the reaction.
+
+SP3 Protein Clean-up
+Always prepare 70% ethanol fresh and get also acetonitrile fresh from the stock bottle.
+1. Transfer 10 µl of lysate (~10 µg of protein) to a PCR tube.
+2. Add 40 µl of 50 mM HEPES to the lysate, followed by 2 µl of beads, mix them well by pipetting.
+3. Immediately add acetonitrile to obtain a final percentage of 50%, (52 µl).
+4. Incubate for 8 minutes at room temperature off the magnetic rack.
+5. Place on magnetic rack and incubate for further 2 minutes at room temperature.
+6. Remove and discard supernatant, on the magnet.
+7. Add 200 µL of 70% ethanol and incubate for 15 seconds on magnetic stand. Remove and discard supernatant.
+8. Add 200 µL of 70% ethanol and incubate for 15 seconds on magnetic stand. Remove and discard supernatant.
+9. Add 180 µL of acetonitrile and incubate for 15 seconds on magnetic stand. Remove and discard supernatant (all droplets) and air dry beads for 30-60 seconds.
+10. For digestion, reconstitute beads in 10 µL of digestion solution (e.g. 50mM HEPES pH 8.0 + 200 ng of trypsin (1:50 enzyme to substrate ratio). It is not necessary to completely homogenize the beads, as they will be stuck to each other and excessive handling will generate bubbles. The cluster will degrade as proteins are digested.
+11. Incubate for 14 hours at 37°C.
+Digested peptides can be recovered from the beads by placing the tube on a magnetic rack and removing the supernatant containing them.
+
+SP3 Peptide Recovery and Preparation for TMT
+1. Vortex and spin your samples then sonicate the tubes 5 minutes in the ultrasound bath. Resuspend
+beads after digest by vortexing and spin shortly.
+2. Place tube on magnetic rack and incubate for further 2 minutes at room temperature.
+3. Transfer supernatant into new PCR tube
+4. Wash the tube with the beads with 10 µl 50 mM HEPES, spin down and place the tube again for 2 minutes on magnet. Note: do not use any amine containing buffer (e.g. TRIS) in this step, as amines will also react with the NHS-group of TMT-labelling reagent.
+5. Combine the supernatants in the new tube.
+Recovered samples can be directly used for TMT labeling.
+
+SP3 TMT-Labelling
+1. Reconstitute the aliquot of TMT labelling reagent in 5 µL of acetonitrile and pipette mix.
+2. Add 4 µl of one TMT label to the digestion mixture and pipette mix. Incubate for 30 min to 1 hour at room temperature.
+3. Add 4 µl 5% hydroxylamine, pipette mix and incubate for 15 minutes at room temperature.
+The isobaric tag serves as a ‘barcode’ that indicates from which sample a peptides derived. Therefore, you can now mix TMT labelled peptides in a 1:1 ratio or you can perform label checks on each sample separately to determine the labelling efficiency and also to compare the overall amount of the samples for later mixing.
+4. Dilute sample with 40 µl Buffer A from OASIS workflow.
+5. Pool all samples for TMT16 multiplexing into a new Eppendorf tube.
+6. Wash PCR tube once more with 40 µl Buffer A and combine to the Eppendorf tube.
+You need to reduce the acetonitrile concentration in the sample before starting the desalting, else the sample would not be able to bind to the C18 material and you lose it.
+Desalting the samples by OASIS
+
+Buffer A
+0.05% formic acid (FA) in water
+
+Buffer B
+80% acetonitrile (CAN), 0.05% FA in water
+
+Reverse phase clean-up step of peptide mix using OASIS HLB µElution Plate, which consist of a Hydrophilic-Lipophilic Balanced reverse phase sorbent. A vacuum is applied for each step: 
+
+Equilibrate the well of an OASIS plate:
+
+Activation of C18 material:
+1. Wash with 100 µl B
+2. Wash with 100 µl B
+
+Equilibration to enable sample binding:
+3. Wash with 100 µl A
+4. Wash with 100 µl A
+
+Sample loading and binding to C18:
+5. Load sample
+
+Desalting step:
+6. Wash with 100 µl A
+7. Wash with 100 µl A
+
+Sample elution & collection:
+8. Place glass vial to collect eluate below OASIS well
+9. Elute with 50 µl B
+10.Elute with 50 µl B
+Dry samples in Speedvac and reconstitute peptides in 1% formic acid supplemented with 4% acetonitrile. Samples are now ready for the injection on a mass spectrometer
+
+References
+EMBL – Proteomics Core Facility
+

From b096cd6410fb933f0bcbcbba361cf6d2e32b8c72 Mon Sep 17 00:00:00 2001
From: saschulz <105273410+saschulz@users.noreply.github.com>
Date: Wed, 11 Oct 2023 16:23:57 +0200
Subject: [PATCH 2/7] Create Metabolite extraction from plant tissue

added SOP
---
 .../Metabolite extraction from plant tissue   | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from plant tissue

diff --git a/docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from plant tissue b/docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from plant tissue
new file mode 100644
index 00000000..b087d91b
--- /dev/null
+++ b/docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from plant tissue	
@@ -0,0 +1,33 @@
+Protocol/MCF/SamplePrep/03: Metabolite extraction from plant tissues  
+
+Sample required:Plant material required: 20-50 mg finely homogenized tissue 
+ 
+Materials and preparations:
+MS grade Methanol (with suitable IS mix 100 ng), MilliQ Water, with suitable internal standards mix 100 ng, HLB (30 mg) SPE columns, SPE assembly, 5% Methanol, 80% methanol 
+Extraction buffer (50 mM sodium phosphate buffer, pH 7.0, containing 0.1%diethyldithiocarbamate)Loading bufferUse 1 ml of the extraction buffer to test the amount of 1M HCl needed for itsacidification to pH 2.7. Prepare the loading buffer by adding twice the amount of1 M HCl per milliliter of extraction buffer. (Addition of 0.5 ml sample extract to 0.5 ml loading buffer must give a pH 2.7)
+
+Note: Keep diluents in chilled condition (0-4oC)  
+
+Sample preparation and metabolite extraction:
+
+1.	Sample Extraction (For Indole acetate metabolites; IAA):  20 to 50 mg of tissues was mixed with 1 ml cold extraction buffer and homogenized using a Mixer Mill MM301 bead mill (Retsch GmbH (http://www.retsch.com)) at a frequency of 25 Hz for 5 min after adding 2 mm ceria-stabilized zirconium oxide beads.
+2.	Add 1 μg of 13C indole acetate (or other suitable internal standards) and vortex well.
+3.	Incubated this plant extracts at 4°C with continuous shaking (20 min) and centrifuge (15 min, 23 000 g at 4°C)
+4.	Transfer the supernatant to a new vial and adjust pH to 2.7 with 1 M HCl
+5.	SPE procedure:
+a.	Prepare SPE vacuum assembly with HLB (30mg) column cartridges.  
+b.	Condition SPE column with 1 mL of methanol and 1mL of water
+c.	Equilibrate the column with 250 μl of 5 mM HCl. (Do not let column dry)
+d.	Load equilibrate column with 0.5 ml loading buffer 
+e.	Load 0.5 ml Sample onto the SPE column, and mix intensely with the loading buffer. Pass the mixture slowly through the HLB sorbent immediately.
+f.	Wash the column with 2 ml of 5% methanol.
+g.	Put clean glass tubes into the manifold rack, and then elute the sample from the column with 2 ml of 80% methanol.
+h.	Collect sample eluent and evaporate the samples to dryness in a SpeedVac concentrator or under nitrogen stream at room temperature.
+6.	Store samples at -80°C till further analysis or ship in dry ice.
+
+7.	Sample are reconstituted in mobile phase (or 50% methanol) before analysis 
+
+
+
+Reference:
+1.	Nov´ak, O., Pˇenˇc´ık, A., Blahouˇsek, O., and Ljung, K. 2016.Quantitative auxin metabolite profiling using stable isotope dilutionUHPLC-MS/MS. Curr. Protoc. Plant Biol. 1:419-430. doi: 10.1002/cppb.20028

From 76cfc93e6b1dd0b774cda4264b65bfcc55991507 Mon Sep 17 00:00:00 2001
From: saschulz <105273410+saschulz@users.noreply.github.com>
Date: Wed, 11 Oct 2023 16:24:48 +0200
Subject: [PATCH 3/7] Create  Metabolite extraction from adherent mammalian
 cells

added SOP
---
 ...e extraction from adherent mammalian cells | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from adherent mammalian cells

diff --git a/docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from adherent mammalian cells b/docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from adherent mammalian cells
new file mode 100644
index 00000000..ad2ce127
--- /dev/null
+++ b/docs/_Experimental-Procedure-Standards-SOPs/Metabolite extraction from adherent mammalian cells	
@@ -0,0 +1,37 @@
+ Protocol/MCF/SamplePrep/01: Metabolite extraction from adherent mammalian cells 
+
+Aim: Aqueous metabolite extraction from mammalian cells or microbial samples for LC-MS analysis 
+
+Sample required:
+Cells required: Cells For cultured cells, use the equivalent of 2–3 million cells. For other sample types a minimum mass of 20 mg is required.
+ 
+Materials:
+MS grade Methanol (with suitable IS mix 100 ng), MilliQ Water, with suitable internal standards mix 100 ng
+
+Note: Keep diluents in chilled condition (0-4oC)  
+Sample preparation and metabolite extraction:
+
+1.	Take 250μl spent growth medium and place it in Eppendorf tubes which already contain 750μl very cold (-80oC) HPLC-grade methanol. (Keep it in case you wish to analyze extracellular metabolites). [optional]
+2.	Aspirate the medium completely.
+3.	Pour 10ml (adjust volume as per the size of dish/ plate) of 10 mM Ammonium acetate (all over the petri dish, wash cells carefully and gently and then discard the washing solution.
+4.	Put the plates on dry ice and add 4 ml of 80% (vol/vol) methanol (or Methanol:acetonitrile:water; 4:4:2) (cooled to - 80°C or on dry ice or liquid nitrogen). (adjust volume as per the size of dish/ plate)
+5.	Incubate the plate at - 80 °C for 20 min. Remove cell plate and keep it on dry ice.
+6.	Scrape the plates on dry ice with cell scraper.
+7.	Transfer the cell lysate/methanol mixture to a 15 ml conical tube (or 1.5 ml / 5 ml eppendorf depending on volumes) on dry ice. If you notice residual cells on the plate, introduce additional washing steps to increase the yield and reduce inter-sample variability
+8.	Add appropriate internal standards
+9.	Vortex for 5 min at maximum speed and make sure that pellet disintegrates and mixed thoroughly with extraction solvent.
+10.	Sample lysis and homogenization (discuss details and alternatives with MCF member). Simplest procedure: place the samples in an ultrasonication bath and sonicate the sample tube for 5 min (Note: Put some ice in sonicator water bath to avoid heating of sample during sonication; rotate/change position of samples during sonication as the energy is not homogeneously distributed in most ultrasonication baths) and vortex briefly after sonication.
+11.	Centrifuge the tube at 14,000g for 10 min at 4–8 °C to pellet the cell debris.
+12.	Transfer the metabolite-containing supernatant to a new 15-ml conical tube (or 1.5 ml eppendorf) on dry ice.
+13.	Optional re-extraction step: Add 500 μl 80% (vol/vol) methanol (- 80°C) to the pellet and resuspend in a 1.5 ml tube and vortex for 1 min.
+○	Resuspending the pellet may be difficult and may require a combination ofvortexing and pipetting up and down (or short period (5 sec) of ultrasonication)
+14.	Spin the tubes at 14,000g for 10 min at 4–8 °C.
+15.	Transfer the supernatant to a tube on dry ice (from Step 13).Divide and transfer 4.5 ml of total extraction buffer into three 1.5-ml microcentrifuge tubes (1.5 ml in each tube). [This step is optional, extracts can be dried directly]
+
+16.	SpeedVac/lyophilize or dry under nitrogen gas to a pellet using no heat.
+17.	Submit dried sample in 1.5 ml eppendorf tube and can be stored at in dried ice.
+18.	Blank control: prepare processed blank sample using same procedure but without biological sample (use water or buffer instead). 
+
+Reference:
+1.	Yuan M, Breitkopf SB, Yang X, Asara JM. A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue. Nat Protoc. 2012 Apr 12;7(5):872-81. doi: 10.1038/nprot.2012.024.
+

From ea481cf9b747ef480d8ef60be2d6713c6da089df Mon Sep 17 00:00:00 2001
From: saschulz <105273410+saschulz@users.noreply.github.com>
Date: Wed, 11 Oct 2023 16:25:33 +0200
Subject: [PATCH 4/7] Create Lipid and fatty acid extraction protocol from
 biological samples

added SOP
---
 ...xtraction protocol from biological samples | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 docs/_Experimental-Procedure-Standards-SOPs/Lipid and fatty acid extraction protocol from biological samples

diff --git a/docs/_Experimental-Procedure-Standards-SOPs/Lipid and fatty acid extraction protocol from biological samples b/docs/_Experimental-Procedure-Standards-SOPs/Lipid and fatty acid extraction protocol from biological samples
new file mode 100644
index 00000000..5eb5a50f
--- /dev/null
+++ b/docs/_Experimental-Procedure-Standards-SOPs/Lipid and fatty acid extraction protocol from biological samples	
@@ -0,0 +1,50 @@
+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 
+
+Sample required:
+Cells required: For cultured cells, use the equivalent of 2–3 million cells or 20-30 mg of microbial mass 
+
+Materials:
+MS grade Methanol, Acetonitrile (ACN), Chloroform, Isopropanol (IPA), MilliQ Water, suitable internal standards mix
+Note: Keep diluents in chilled condition (0-4oC)
+
+Procedure for Lipid extraction: 
+MeOH: Chloroform extraction
+(Caution: use only glass vials, syringe.  No plastic items should be in contact with Chloroform)
+1.	Add 200 µL of cold methanol (containing internal standards mix) for 106 cells or 25 mg microbial culture (in 2 mL glass vial)
+2.	Vortex and mix thoroughly for protein precipitation 
+3.	Add 500 µL of chloroform (with glass syringe) and vortex and keep at cold for 10 min 
+4.	Add 200 µL water for phase separation 
+5.	Vortex and keep at cold for 10 min
+6.	Centrifuge at 600 rpm for 5 min (using 15- or 50-mL falcon tubes inserted with glass vials)
+7.	Carefully remove bottom Chloroform layer of 300 µL using syringe and transfer to new amber colour glass vial (with syringe)
+8.	Keep it at speedvac for 20 min at RT or dry under nitrogen gas stream 
+9.	Dried samples can be stored or shipped in dry ice for analysis.
+10.	Reconstitute is dried sample in IPA:MeOH (1:1)
+11.	Blank control: prepare processed blank samples using the same procedure but without biological sample (use water or buffer instead).
+
+
+Note: Method of measurement of cellular/microbial mass should be established with biologist/ microbiologist depending on experimental design. The method can be biomass weight or OD measurements which can be further used for normalization of lipid levels. Similar decision should be made for quenching procedures
+
+Reference:
+Susan S. Bird, Vasant R. Marur, Matthew J. Sniatynski, Heather K. Greenberg, and Bruce S. Kristal., Serum Lipidomics Profiling using LC-MS and High Energy Collisional Dissociation Fragmentation: Focus on Triglyceride Detection and Characterization. Anal Chem. 2011 September 1; 83(17): 6648–6657. doi:10.1021/ac201195d. 
+
+
+
+
+
+Specific instructions for homogenization of frozen tissues (eg; liver) prior to lipid extraction 
+1)	Starting with frozen tissue*, grind the tissue to a powder while frozen using a hand-held ceramic mortar and pestle. The mortar and pestle (any other apparatus eg; tweezers)  should be liquid nitrogen cooled before and should be kept cold throughout the process. A CryoMill can also be used for the homogenization of the tissue. 
+
+2)	Weigh the powder into a tared eppendorf tube. Keep track of the tissue weights as you need to correct for tissue weight (normalize) when resuspending the samples prior to LC-MS analysis
+
+3)	Extract lipids using the method above Protocol/MCF/SamplePrep/02 
+
+4)	Re-extraction: After the initial extraction, perform a second extraction step of the tissue with 2:1 Chloroform: Methanol (~ 700μL) and combine the bottom layer with the layer from step 3. 
+
+5)	Dry the bottom layer under a nitrogen stream.
+
+*It is difficult to process tissue samples at weights below 10 mg, so aim for at least 10 mg of tissue to start with 
+
+

From eb5a369b16d4ee4fc6fa21b62656aa2a3d447dde Mon Sep 17 00:00:00 2001
From: saschulz <105273410+saschulz@users.noreply.github.com>
Date: Wed, 11 Oct 2023 16:26:12 +0200
Subject: [PATCH 5/7] Create DNA and RNA kits by sample

added SOP
---
 .../DNA and RNA kits by sample                | 92 +++++++++++++++++++
 1 file changed, 92 insertions(+)
 create mode 100644 docs/_Experimental-Procedure-Standards-SOPs/DNA and RNA kits by sample

diff --git a/docs/_Experimental-Procedure-Standards-SOPs/DNA and RNA kits by sample b/docs/_Experimental-Procedure-Standards-SOPs/DNA and RNA kits by sample
new file mode 100644
index 00000000..8b707362
--- /dev/null
+++ b/docs/_Experimental-Procedure-Standards-SOPs/DNA and RNA kits by sample	
@@ -0,0 +1,92 @@
+Nucleic Acid extraction kits
+
+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
+
+
+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).
+4. Gao, L. et al. Polymicrobial periodontal disease triggers a wide radius of effect and unique virome. npj Biofilms and Microbiomes 2020 6:1 6, 1–13 (2020).
+5. Majumder, R., Sutcliffe, B., Taylor, P. W. & Chapman, T. A. Fruit host-dependent fungal communities in the microbiome of wild Queensland fruit fly larvae. Scientific Reports 2020 10:1 10, 1–12 (2020).
+6. Ellison, S., Knapp, R. & Vredenburg, V. Longitudinal patterns in the skin microbiome of wild, individually marked frogs from the Sierra Nevada, California. ISME Communications 2021 1:1 1, 1–11 (2021).
+7. Kim, H. J. et al. Aged related human skin microbiome and mycobiome in Korean women. Scientific Reports 2022 12:1 12, 1–11 (2022).
+8. Ogai, K. et al. Skin microbiome profile of healthy Cameroonians and Japanese. Scientific Reports 2022 12:1 12, 1–8 (2022).
+9. Chaudhari, D. S. et al. Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age. Scientific Reports 2020 10:1 10, 1–13 (2020).
+10. Scanes, E. et al. Microbiomes of an oyster are shaped by metabolism and environment. Scientific Reports 2021 11:1 11, 1–7 (2021).
+11. Sousa, R. et al. Major ocean currents may shape the microbiome of the topshell Phorcus sauciatus in the NE Atlantic Ocean. Scientific Reports 2021 11:1 11, 1–11 (2021).
+12. Mulec, J. et al. Microbiota entrapped in recently-formed ice: Paradana Ice Cave, Slovenia. Scientific Reports 2021 11:1 11, 1–12 (2021).
+13. Goolam Mahomed, T. et al. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Scientific Reports 2021 11:1 11, 1–12 (2021).
+14. Custodio, M. et al. Microbial diversity in intensively farmed lake sediment contaminated by heavy metals and identification of microbial taxa bioindicators of environmental quality. Scientific Reports 2022 12:1 12, 1–12 (2022).
+15. Kursa, O., Tomczyk, G., Sawicka-Durkalec, A., Giza, A. & Słomiany-Szwarc, M. Bacterial communities of the upper respiratory tract of turkeys. Scientific Reports 2021 11:1 11, 1–11 (2021).
+16. Satjarak, A., Golinski, G. K., Trest, M. T. & Graham, L. E. Microbiome and related structural features of Earth’s most archaic plant indicate early plant symbiosis attributes. Scientific Reports 2022 12:1 12, 1–11 (2022).
+17. Park, J. Y. et al. Dysbiotic change in gastric microbiome and its functional implication in gastric carcinogenesis. Scientific Reports 2022 12:1 12, 1–11 (2022).
+18. Eun, Y. G. et al. Oral microbiome associated with lymph node metastasis in oral squamous cell carcinoma. Scientific Reports 2021 11:1 11, 1–10 (2021).
+19. Shetty, S. A. et al. Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria. npj Biofilms and Microbiomes 2022 8:1 8, 1–13 (2022).
+20. Hannula, S. E. et al. Persistence of plant-mediated microbial soil legacy effects in soil and inside roots. Nature Communications 2021 12:1 12, 1–13 (2021).
+21. Zheng, X. et al. Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. The ISME Journal 2022 16:5 16, 1397–1408 (2022).
+22. Morin, L. et al. Colonization kinetics and implantation follow-up of the sewage microbiome in an urban wastewater treatment plant. Scientific Reports 2020 10:1 10, 1–14 (2020).
+23. Yahara, K. et al. Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria. Nature Communications 2021 12:1 12, 1–12 (2021).
+24. Lee, C. Z. et al. The gut virome in two indigenous populations from Malaysia. Scientific Reports 2022 12:1 12, 1–10 (2022).
+25. Liang, G. et al. The stepwise assembly of the neonatal virome is modulated by breastfeeding. Nature 2020 581:7809 581, 470–474 (2020).
+26. Chehoud, C. et al. Transfer of viral communities between human individuals during fecal microbiota transplantation. mBio 7, (2016).
+27. Zhang, F. et al. Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease. Nature Communications 2021 12:1 12, 1–11 (2021).
+28. Humphrey, P. T. & Whiteman, N. K. Insect herbivory reshapes a native leaf microbiome. Nature Ecology & Evolution 2020 4:2 4, 221–229 (2020).
+29. Ali, R. et al. Characterization of the virome associated with Haemagogus mosquitoes in Trinidad, West Indies. Scientific Reports 2021 11:1 11, 1–13 (2021).
+30. Wille, M. et al. Sustained RNA virome diversity in Antarctic penguins and their ticks. The ISME Journal 2020 14:7 14, 1768–1782 (2020).
+31. Xu, L. et al. Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nature Communications 2021 12:1 12, 1–17 (2021).
+32. Arroyo Mühr, L. S., Dillner, J., Ure, A. E., Sundström, K. & Hultin, E. Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics. Scientific Reports 2021 11:1 11, 1–12 (2021).
+

From 8e71e6aaa3094a1183537dfd16f22b99654e08ba Mon Sep 17 00:00:00 2001
From: saschulz <105273410+saschulz@users.noreply.github.com>
Date: Wed, 11 Oct 2023 16:26:58 +0200
Subject: [PATCH 6/7] Create Sample Collection and Storage by Sample

added SOP
---
 .../Sample Collection and Storage by Sample   | 105 ++++++++++++++++++
 1 file changed, 105 insertions(+)
 create mode 100644 docs/_Experimental-Procedure-Standards-SOPs/Sample Collection and Storage by Sample

diff --git a/docs/_Experimental-Procedure-Standards-SOPs/Sample Collection and Storage by Sample b/docs/_Experimental-Procedure-Standards-SOPs/Sample Collection and Storage by Sample
new file mode 100644
index 00000000..2f4750be
--- /dev/null
+++ b/docs/_Experimental-Procedure-Standards-SOPs/Sample Collection and Storage by Sample	
@@ -0,0 +1,105 @@
+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.
+Protein samples stored at -80ºC will be frozen. As repeated freeze-thaw cycles usually have a negative influence on protein samples, it is best to prepare small-sized, single-use aliquots that will be used up during the course of an experiment. 5-10% glycerol or other additives that protect against the effect of freezing and thawing can be added as well. After preparing your protein sample aliquots, it is important to flash-freeze them in liquid nitrogen before importing them into the -80ºC freezer for long-term storage. Many proteins are stable for months to years when stored under appropriate conditions at -80°C, but the exact time frame varies from protein to protein and should be determined experimentally.
+
+Sponges2 – washed three times with filter-sterilised natural seawater, one fragment placed in 70% ethanol, one fragment placed in RNALater, stored at -20°C
+
+Seawater3 – filtered through a 200 µm, then a 20 µm mesh, then vacuum filtered through a 0.8 µm filter, then a 0.2 µm filter, flash frozen in liquid nitrogen & stored at -80°C (all done with ~4h; water at 4°C during processing)
+
+Seawater4 – filtered through a 0.2 µm filter, filter stored in 2 ml tubes containing lysis buffer (EDTA 40 mmol l−1 pH 8.0, Tris-HCl 50 mmol l−1 pH 8.0, sucrose 0.75 mol l−1) flash frozen in liquid nitrogen, filtered & unfiltered water stored in 15 ml falcons at -20°C
+
+Prokaryotes in sea water5 – water sampled without filtration, 2% final concentration glutaraldehyde added, stored at 4°C for 15 min in the dark, flash-frozen in liquid nitrogen and stored at -80°C
+
+Swedish cervical biobank6 – stored in liquid at -25°C, using liquid-based cytology cells suspended and fixed in Thinprep (TP) containing 20 ml PreservCyt (ThinPrep Hologic, Boxborough, MA)
+4 ml of liquid-based cytology sample from the bottom of the patient tube is transferred into a conical tube and allowed to sediment for 30 min
+300 µl of the sediment are transferred to a cryotube and stored at -25°C
+
+Pooled tear collection7 – centrifuged at 270 g for 3 min, supernatant stored in 1.5 ml microcentrifuge tubes at -80°C
+
+Mosquitos8 – human bait adult catching method, pool 3-5 mosquitos, store at -80°C
+
+Oral swabs9 – after collection swab is immersed in 10:1 Tris-EDTA buffer immediately and stored at −80 °C
+
+Fruit fly larvae10 – sterilise larvae with a solution of 0.5 % Tween 80, 0.5 % sodium hypochlorite and 80 % ethanol for 30 sec, rinse them 3 times in PBS for 30 sec, use sterile pestle to crush larvae and store in BHI containing 20 % glycerol at -80°C
+
+Turkey Trachea swabs11 – placed in 1 ml PBS, then stored at -20°C
+
+Frog toes12 – stored in sterile 1.5 ml tubes at -80°C
+
+Leaves13 – surface sterilise: rinse for 5 sec 95% ethanol, 30 sec in 70% ethanol, 30 sec in 10% bleach, followed by three 2-minute washes in sterile water, air-dry for 5 min, then add to 2 ml tube containing 350 µL 10 mM MgSO4 and a sterile 5 mm steel ball and homogenise using a TissueLyser (QIAGEN) run at max speed (50 Hz) for up to 60 sec, then flash freeze in liquid nitrogen and store at -80°C
+
+Atlantic salmon14 – dissection samples placed in RNAlater and stored at -80°C
+
+Yoghurt15 – after purchase, samples were placed immediately at 4°C for transport and within 12 h stared at -80°C
+
+Activated sludge from wastewater16 – collected samples stored at 4°C for transport, within 6 h centrifuged at 6 500 g for 15 min at 4°C, supernatant removed and pellets stored at -20°C
+
+Penguin cloacal swaps17 – placed in tubes containing viral transport medium (brain heart infusion [BHI] broth-based medium [Oxoid] with 0.3 mg/ml penicillin, 5 mg/ml streptomycin, 0.1 mg/ml gentamicin, and 2.5 μg/ml amphotericin B), kept on ice for 4 hours, then stored at -80°C
+
+Antarctic ticks17 – collected from rocks, placed in RNALater and stored at -80°C within 4-8 h of collection
+
+Frog swabbing18 – rinse caught frog with 50 ml sterilised water to remove transient bacteria, swab entire skin surface with a sterile Dacron swab for 30 sec, place swab in microcentrifuge tube containing PBS and store on ice, then transfer to -80°C storage
+
+Invertebrates19 – whole samples are stored in 80 % ethanol, in fridge for short-term storage, and in -20°C freezer for long-term storage.
+
+Hooded seal brain19 – whole samples are placed in 4°C glucose artificial cerebrospinal fluid (aCSF) saturated with 95 % O2 - 5 % CO2. After experiment (induced normoxia and hypoxia), tissues were stored in RNAlater stabilisation fluid (Life Technologies, USA) and kept at 4°C.
+
+Saliva20 - passive drooling procedure in sterile 50 ml screw top tubes (approximately 3 ml of saliva per sample). About 30 minutes before collection, all volunteers performed a mouth rinse with drinking water. Samples were vortexed before 2 ml of each was centrifuged at 10,000 × g for 10 minutes to collected the bacterial pellets. Total DNA was extracted using the PowerSoil DNA Isolation Kit (MoBio), according to manufacturer’s instructions. DNA was stored at −20 °C until used.
+
+Skin swab20 - Skin samples were collected using Catch-All-Swabs (Epicentre Technologies, Wisconsin, USA) shortly after birth but before the skin-to-skin contact with the infant, by swabbing the upper area of the maternal breast (intermammary cleft). After pre-moistening with 2 ml SCF-1 buffer (50 mM Tris buffer, pH 7.6, 1mM EDTA, pH 8.0, and 0.5% Tween-20) (Human Microbiome Project Consortium, 2012) contained in a 15 ml sterile screw top collection tube (Sarstedt, Nümbrecht, Germany), the swab head was rubbed back and forth for approximately 30 seconds over the area (repeating twice) before the swab was returned to the buffered solution. The lower part of the swab was broken to ensure closure of the tube (see below). After sampling, deterge the sampled area with a clean pad of cotton and water. 
+
+
+
+
+
+
+
+
+
+
+Vaginal swabs20 - Skin samples were collected using Catch-All-Swabs (Epicentre Technologies, Wisconsin, USA). The swab was rubbed 5 times, with a circular motion, in the vaginal introitus and then the swab head was placed in a 15 ml sterile screw top collection tube containing 2 ml SCF-1 buffer (see photos above).
+
+Tongue dorsum swabs20 – Skin samples were collected using Catch-All-Swabs (Epicentre Technologies, Wisconsin, USA). Samples were collected by rubbing a swab on the central area of the back of the tongue for approximately 5 seconds. The swab head was then placed in a 15 ml collection tube containing 2 ml SCF-1 buffer (see photos above). Samples were collected while wearing protective disposable gloves to avoid skin contamination. 
+
+Maternal Milk (without glycerol)20
+Minimum of 2ml of milk was self-collected by the mothers in sterile falcon tubes while wearing disposable gloves. No buffer was added. Samples were stored at -4C right after collection and moved to -80C within a week. Note that for colostrum and other milk samples within the first week of life the 2ml min quantity might not be possible. In that case, the mother collected whatever quantity was possible in 10 min timespan. 
+
+Maternal Milk (with glycerol)20
+Minimum of 2ml of milk was self-collected by the mothers in sterile falcon tubes with added 20% glycerol while wearing disposable gloves. Samples without were stored at -20C for cultivation experiments. Note that for colostrum and other milk samples within the first week of life the 2ml min quantity might not be possible. In that case, the mother collected whatever quantity was possible in 10 min timespan.
+
+Stool samples20 – samples were self-collected using collection tubes specific for faecal material (Sarstedt, Nümbrecht, Germany). Toilet paper was placed at the bottom of the WC, to prevent stool samples from sinking and getting contaminated. The collection was performed at the upper part of the feces, the one not in contact with the toilet paper, WC walls or other material. Subjects were instructed, whenever possible, to urinate before evacuating the stools. Samples were collected in variable quantity, depending on availability (meconium is usually only one spoon). Once collected the tube was placed at -4C as soon as possible, and then transferred to -80C within a week.  
+
+
+
+
+
+
+
+Faeces/gut content21 – flash freeze in liquid nitrogen and store at -80°C (dissolve in Stool DNA Stabilizer (INVITEK Molecular) while thawing; or if you have more time dissolve in Stool DNA Stabilizer right after collection and normally freeze and store at -80°C) 
+
+
+References
+1. Protein purification – Protein Expression and Purification Core Facility. https://www.embl.org/groups/protein-expression-purification/services/protein-purification/.
+2. Ruocco, N. et al. Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis. Scientific Reports 2021 11:1 11, 1–12 (2021).
+3. Acinas, S. G. et al. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Communications Biology 2021 4:1 4, 1–15 (2021).
+4. Michoud, G. et al. Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline. The ISME Journal 2021 15:8 15, 2351–2365 (2021).
+5. Baltar, F. et al. Specific Effect of Trace Metals on Marine Heterotrophic Microbial Activity and Diversity: Key Role of Iron and Zinc and Hydrocarbon-Degrading Bacteria. Front Microbiol 9, 3190 (2018).
+6. Perskvist, N., Norman, I., Eklund, C., Litton, J. E. & Dillner, J. The Swedish Cervical Cytology Biobank: Sample Handling and Storage Process. https://home.liebertpub.com/bio 11, 19–24 (2013).
+7. Willis, K. A. et al. The closed eye harbours a unique microbiome in dry eye disease. Scientific Reports 2020 10:1 10, 1–10 (2020).
+8. Ali, R. et al. Characterization of the virome associated with Haemagogus mosquitoes in Trinidad, West Indies. Scientific Reports 2021 11:1 11, 1–13 (2021).
+9. Gao, L. et al. Polymicrobial periodontal disease triggers a wide radius of effect and unique virome. npj Biofilms and Microbiomes 2020 6:1 6, 1–13 (2020).
+10. Majumder, R., Sutcliffe, B., Taylor, P. W. & Chapman, T. A. Fruit host-dependent fungal communities in the microbiome of wild Queensland fruit fly larvae. Scientific Reports 2020 10:1 10, 1–12 (2020).
+11. Kursa, O., Tomczyk, G., Sawicka-Durkalec, A., Giza, A. & Słomiany-Szwarc, M. Bacterial communities of the upper respiratory tract of turkeys. Scientific Reports 2021 11:1 11, 1–11 (2021).
+12. Boyle, D. G., Boyle, D. B., Olsen, V., Morgan, J. A. T. & Hyatt, A. D. Rapid quantitative detection of chytridiomycosis (Batrachochytrium dendrobatidis) in amphibian samples using real-time Taqman PCR assay. Dis Aquat Organ 60, 141–148 (2004).
+13. Humphrey, P. T. & Whiteman, N. K. Insect herbivory reshapes a native leaf microbiome. Nature Ecology & Evolution 2020 4:2 4, 221–229 (2020).
+14. Karlsen, C. et al. Feed microbiome: confounding factor affecting fish gut microbiome studies. ISME Communications 2022 2:1 2, 1–4 (2022).
+15. Islam, S. M. R. et al. Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh. Scientific Reports 2021 11:1 11, 1–15 (2021).
+16. Morin, L. et al. Colonization kinetics and implantation follow-up of the sewage microbiome in an urban wastewater treatment plant. Scientific Reports 2020 10:1 10, 1–14 (2020).
+17. Wille, M. et al. Sustained RNA virome diversity in Antarctic penguins and their ticks. The ISME Journal 2020 14:7 14, 1768–1782 (2020).
+18. Ellison, S., Knapp, R. & Vredenburg, V. Longitudinal patterns in the skin microbiome of wild, individually marked frogs from the Sierra Nevada, California. ISME Communications 2021 1:1 1, 1–11 (2021).
+
+19. Courtesy of Justine Vandendorpe
+20. Courtesy of Pamela Feretti
+21. Courtesy of Johannes Masson
+

From b6361064b37b2108203059e7c3c4f73b7ca9a969 Mon Sep 17 00:00:00 2001
From: mahdi-robbani <shahriyar.robbani@embl.de>
Date: Mon, 22 Jan 2024 16:35:19 +0100
Subject: [PATCH 7/7] modified file names

---
 ...ample => 04-DNA-and-RNA-kits-by-sample.md} | 119 ++++++++++--------
 ...ction-protocol-from-biological-samples.md} |   7 ++
 ...traction-from-adherent-mammalian-cells.md} |   9 +-
 ...etabolite-extraction-from-plant-tissue.md} |   8 ++
 ... 08-Proteomics-TMT-labelled-SP3-method.md} |   8 ++
 ...ample-Collection-and-Storage-by-Sample.md} |   7 ++
 6 files changed, 102 insertions(+), 56 deletions(-)
 rename docs/_Experimental-Procedure-Standards-SOPs/{DNA and RNA kits by sample => 04-DNA-and-RNA-kits-by-sample.md} (62%)
 rename docs/_Experimental-Procedure-Standards-SOPs/{Lipid and fatty acid extraction protocol from biological samples => 05-Lipid-and-fatty-acid-extraction-protocol-from-biological-samples.md} (95%)
 rename docs/_Experimental-Procedure-Standards-SOPs/{Metabolite extraction from adherent mammalian cells => 06-Metabolite-extraction-from-adherent-mammalian-cells.md} (93%)
 rename docs/_Experimental-Procedure-Standards-SOPs/{Metabolite extraction from plant tissue => 07-Metabolite-extraction-from-plant-tissue.md} (94%)
 rename docs/_Experimental-Procedure-Standards-SOPs/{Proteomics - TMT-labelled SP3 method => 08-Proteomics-TMT-labelled-SP3-method.md} (97%)
 rename docs/_Experimental-Procedure-Standards-SOPs/{Sample Collection and Storage by Sample => 09-Sample-Collection-and-Storage-by-Sample.md} (98%)

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
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index b087d91b..05283d0d 100644
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+++ 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
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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
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@@ -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.