Adjust new files to the new contribution standard

NFDI4Microbiota · Oct 31, 2024 · b62ee24 · b62ee24
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diff --git a/...-Procedure-Standards-SOPs/00_sop-template → ...ocedure-Standards-SOPs/00_sop-template.md b/...-Procedure-Standards-SOPs/00_sop-template → ...ocedure-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,
@@ -42,13 +45,13 @@ Here are a few examples:
   url = {https://doi.org/10.1038/s41598-019-45173-4}
 }
 
-# Protocol
+## Protocol
+
+---
 
 Add your protocol here.
 
 ##Method
 
 ##Material
 
-# References
-{% bibliography --cited_in_order %}
diff --git a/...mental-Procedure-Standards-SOPs/03-viral-purification-from-bacterial-culture.md b/...mental-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.
diff --git a/...dia-freezing-faecal-samples-recultivation → ...-freezing-faecal-samples-recultivation.md b/...dia-freezing-faecal-samples-recultivation → ...-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/...ure-Standards-SOPs/11-biobank-fmt-samples → ...-Standards-SOPs/11-biobank-fmt-samples.md b/...ure-Standards-SOPs/11-biobank-fmt-samples → ...-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/...re-Standards-SOPs/12-godon-dna-extraction → ...Standards-SOPs/12-godon-dna-extraction.md b/...re-Standards-SOPs/12-godon-dna-extraction → ...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 %}