diff --git a/docs/_Experimental-Procedure-Standards-SOPs/00_sop-template b/docs/_Experimental-Procedure-Standards-SOPs/00_sop-template.md similarity index 93% rename from docs/_Experimental-Procedure-Standards-SOPs/00_sop-template rename to docs/_Experimental-Procedure-Standards-SOPs/00_sop-template.md index 42b86cf..04c2db5 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/00_sop-template +++ b/docs/_Experimental-Procedure-Standards-SOPs/00_sop-template.md @@ -9,7 +9,7 @@ hide: true This is a template document on how to add templates to the knowledge base. Please create a copy and adapt accordingly. -# Metadata +## Metadata | Title | Category | Adapated and used by | last accessed | Link to protocol | Primary origin for protocol | | ------ | ------ | ------ | ------ | ------ |------ | @@ -18,7 +18,10 @@ Collaborative Research Center 1382, Project Q02 “Integrative Microbiota Analys {: .table .table-hover} -# add references to the bib file add: +## add references to the bib file add: + +--- + Here are a few examples: @misc{fmt_media, @@ -42,7 +45,9 @@ Here are a few examples: url = {https://doi.org/10.1038/s41598-019-45173-4} } -# Protocol +## Protocol + +--- Add your protocol here. @@ -50,5 +55,3 @@ Add your protocol here. ##Material -# References -{% bibliography --cited_in_order %} diff --git a/docs/_Experimental-Procedure-Standards-SOPs/03-viral-purification-from-bacterial-culture.md b/docs/_Experimental-Procedure-Standards-SOPs/03-viral-purification-from-bacterial-culture.md index 34a29be..2a5da92 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/03-viral-purification-from-bacterial-culture.md +++ b/docs/_Experimental-Procedure-Standards-SOPs/03-viral-purification-from-bacterial-culture.md @@ -19,4 +19,7 @@ docs_css: markdown 11. Store at 4°C ## Source + +--- + In-house protocol provided by Sarah Schulz. \ No newline at end of file diff --git a/docs/_Experimental-Procedure-Standards-SOPs/10-media-freezing-faecal-samples-recultivation b/docs/_Experimental-Procedure-Standards-SOPs/10-media-freezing-faecal-samples-recultivation.md similarity index 93% rename from docs/_Experimental-Procedure-Standards-SOPs/10-media-freezing-faecal-samples-recultivation rename to docs/_Experimental-Procedure-Standards-SOPs/10-media-freezing-faecal-samples-recultivation.md index d500e4c..4a33328 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/10-media-freezing-faecal-samples-recultivation +++ b/docs/_Experimental-Procedure-Standards-SOPs/10-media-freezing-faecal-samples-recultivation.md @@ -6,7 +6,7 @@ docs_css: markdown hide: false --- -# Metadata +## Metadata | Title | Adapated and used by | last accessed | Link to protocol | Primary origin for protocol | | ------ | ------ | ------ | ------ | ------ | @@ -15,8 +15,9 @@ Collaborative Research Center 1382, Project Q02 “Integrative Microbiota Analys {: .table .table-hover} -# Protocol +## Protocol +--- 1. Make normal saline: 9.0 g/L NaCl 2. Dissolve Maltodextrin and Trehalose in normal saline at 40 °C, to respective final concentrations @@ -31,15 +32,11 @@ For 100 mL: 0.5 g | Ascorbic acid | 0.05 g | L-Cystein | -## Material +### Material + - Maltodextrin [PubChem SID: 481109074](https://pubchem.ncbi.nlm.nih.gov/substance/481109074) - Trehalose - L-Cystein - Ascorbic acid - NaCl - Water (MQ/DEPC) - - -# References -{% bibliography --cited_in_order %} - diff --git a/docs/_Experimental-Procedure-Standards-SOPs/11-biobank-fmt-samples b/docs/_Experimental-Procedure-Standards-SOPs/11-biobank-fmt-samples.md similarity index 98% rename from docs/_Experimental-Procedure-Standards-SOPs/11-biobank-fmt-samples rename to docs/_Experimental-Procedure-Standards-SOPs/11-biobank-fmt-samples.md index ebf15b8..8a10fb0 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/11-biobank-fmt-samples +++ b/docs/_Experimental-Procedure-Standards-SOPs/11-biobank-fmt-samples.md @@ -6,7 +6,7 @@ docs_css: markdown hide: true --- -# Metadata +## Metadata | Title | Category | Adapated and used by | last accessed | Link to protocol | Primary origin for protocol | | ------ | ------ | ------ | ------ | ------ |-------| @@ -15,7 +15,9 @@ Collaborative Research Center 1382, Project Q02 “Integrative Microbiota Analys {: .table .table-hover} -# Protocol +## Protocol + +--- For each sample (001-NNN), label 50 x 1,5 mL Eppendorf Tubes as follows (example for project acronym “Cultimic”): @@ -74,6 +76,3 @@ Collect questionnaires and enter metadata into the protected, study-specific spr - 1 mL syringes - 50 mL Falcon tubes - Pipet tips with wide opening 1250µL; VWR (613-0751) - -# References -{% bibliography --cited_in_order %} diff --git a/docs/_Experimental-Procedure-Standards-SOPs/12-godon-dna-extraction b/docs/_Experimental-Procedure-Standards-SOPs/12-godon-dna-extraction.md similarity index 96% rename from docs/_Experimental-Procedure-Standards-SOPs/12-godon-dna-extraction rename to docs/_Experimental-Procedure-Standards-SOPs/12-godon-dna-extraction.md index 01a49ca..915fca3 100644 --- a/docs/_Experimental-Procedure-Standards-SOPs/12-godon-dna-extraction +++ b/docs/_Experimental-Procedure-Standards-SOPs/12-godon-dna-extraction.md @@ -7,7 +7,7 @@ hide: true --- -# Metadata +## Metadata | Title | Category | Adapated and used by | last accessed | Link to protocol | Primary origin for protocol | | ------ | ------ | ------ | ------ | ------ |------ | @@ -17,16 +17,18 @@ Collaborative Research Center 1382, Project Q02 “Integrative Microbiota Analys *Consider accessing the protocol for a donwloadable PDF version.* -# Protocol +## Protocol -## Prepare: +--- + +### Prepare: - TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA) - Bead-beater-tubes (with 500 mg+/- 10 mg Zirconia/Silicia beads, autoclaved) - 4M Guanidinethiocyanate in 0,1M Tris pH 7,5 (consider appropriate disposal) - 5 % N-laurolylsarcosine in PBS (Dulbecco’s phosphate Buffered Saline) (consider appropriate disposal) -## Sample preparation: +### Sample preparation: Consider first if you want to use the enzymatic lysis step! - For extraction from bacterial culture: Take 2 ml of a well grown culture, centrifuge it at 12.000 x g for 10 min, and discard the supernatant @@ -36,7 +38,7 @@ thaw at room temperature. temperature - If protocol is used with enzymatic step do not use DNA Stabilizer -## DNA Isolation: +### DNA Isolation: **For enzymatic extraction** Prepare Lysozyme-Solution (TE Buffer with 15 µg/µl Lysozyme): mass Lysozyme = (#Samples(+1)) * 7.5 mg @@ -67,7 +69,7 @@ Centrifuge at 15.000 x g, 4 °C, 3 min heat up DE) 11. Proceed with the NucleoSpin® gDNA Clean-up follow protocol -##Material +### Material - ProteinaseK; Carl Roth (7528.1) - NucleoSpin® gDNA Clean-up; Macherey-Nagel (740230.250) @@ -78,6 +80,3 @@ heat up DE) - TE buffer; Sigma-Aldrich (T9285-100ML) - Poly(vinylpolypyrrolidone); Sigma-Aldrich (P5288-100G) - 1.5 mL and 2 mL Eppendorf tubes - -# References -{% bibliography --cited_in_order %}