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upgrade run 1 to test how it will look
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nkurtys committed Oct 11, 2024
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2 changes: 1 addition & 1 deletion docs/_Experimental-Procedure-Standards-SOPs/01.1-introduction.md
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Expand Up @@ -28,5 +28,5 @@ SOPs serve as valuable educational resources for training new researchers and st

The listed experimental SOPs that can be found on this Knowledge Base have been collected by NFDI4Microbiota's consortia members and participants from either (1) well-established and published sources or (2) consist of well-running in-house protocols that have been recently established by various research consortia and their domain expert with wet-lab experiences.

# Get Help
## Get Help
If you have any further questions about the management and analysis of your microbial research data, please contact us: [[email protected]](mailto:[email protected]) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/))
2 changes: 1 addition & 1 deletion docs/_Experimental-Procedure-Standards-SOPs/02-external-sops.md
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Expand Up @@ -23,5 +23,5 @@ This page lists well-established and tested protocols from the International Hum
|ITS Illumina Amplicon Protocol| Earth Microbiome | DNA Sequencing | [ITS Illumina Amplicon Protocol](https://www.protocols.io/view/emp-its-illumina-amplicon-protocol-14egnqypg5dy/v1) |
{: .table .table-hover}

# Get Help
## Get Help
If you have any further questions about the management and analysis of your microbial research data, please contact us: [[email protected]](mailto:[email protected]) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/))
8 changes: 4 additions & 4 deletions ...mental-Procedure-Standards-SOPs/03-viral-purification-from-bacterial-culture.md
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Expand Up @@ -5,7 +5,7 @@ layout: default
docs_css: markdown
---

# Protocol
## Protocol
1. Centrifuge 40 ml of bacterial culture infected with phage at 6000 g for 30 min, remove the supernatant and filter it through a 0.45 μm syringe filter
2. Centrifuge the filtrate at 35 000 g for 4 h, remove the supernatant and re-suspend the pellet in 600 μl SM buffer
3. Add 2 μl of DNAse I and 20 μl of 10x DNAse buffer and incubate at 37°C for 1.5 h
Expand All @@ -18,8 +18,8 @@ docs_css: markdown
10. Remove the supernatant and re-suspend the pellet in 100 μl TE buffer
11. Store at 4°C

# Source
In-house protocol provided by Sarah Schulz
## Source
In-house protocol provided by Sarah Schulz.

# Get Help
## Get Help
If you have any further questions about the management and analysis of your microbial research data, please contact us: [[email protected]](mailto:[email protected]) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/))
10 changes: 6 additions & 4 deletions docs/_Experimental-Procedure-Standards-SOPs/04-dna-and-rna-kits-by-sample.md
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---


# Nucleic Acid extraction kits
## Nucleic Acid extraction kits

## DNA extraction
### DNA extraction

- Sponges - QIAamp® DNA Micro kit (QIAGEN){% cite Ruocco_2021 %}
- Sponges –DNeasy® PowerSoil® Pro Kit (QIAGEN){% cite Ruocco_2021 %}
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- Bacterial DNA from cultures (automated) - GenFind v3 Kit (Beckman Coulter) - in house protocol provided by Nicole Treichel
- Bacterial DNA from low biomass (eg. FACS sorted) samlpes – mericon DNA Bacteria Kit (Qiagen)- in house protocol provided by Nicole Treichel

## RNA extraction
### RNA extraction
- Mosquitos - TRIzol LS (Invitrogen) – purified with RNeasy MinElute Cleanup Kit (Qiagen){% cite Ali_2021 %}
- Sea Water - RNeasy mini kit (Qiagen){% cite Martínez-Pérez._2022 %}
- Antarctic ticks - MagMax mirVana™ Total RNA isolation Kit (ThermoFisher Scientific){% cite Willis_2020 %}
Expand All @@ -64,7 +64,9 @@ docs_css: markdown
- Bile samples - ZymoBIOMICS DNA/RNA Miniprep Kit - in house protocol provided by Nicole Treichel
- mouse small intestine content - ZymoBIOMICS DNA/RNA Miniprep Kit - in house protocol provided by Nicole Treichel

# Get Help
---

## Get Help
If you have any further questions about the management and analysis of your microbial research data, please contact us: [[email protected]](mailto:[email protected]) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/))

## References
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2 changes: 1 addition & 1 deletion ...rds-SOPs/05-lipid-and-fatty-acid-extraction-protocol-from-biological-samples.md
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Expand Up @@ -47,7 +47,7 @@ Specific instructions for homogenization of frozen tissues (eg; liver) prior to

*It is difficult to process tissue samples at weights below 10 mg, so aim for at least 10 mg of tissue to start with

# Get Help
## Get Help
If you have any further questions about the management and analysis of your microbial research data, please contact us: [[email protected]](mailto:[email protected]) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/))

## References
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2 changes: 1 addition & 1 deletion ...cedure-Standards-SOPs/06-metabolite-extraction-from-adherent-mammalian-cells.md
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Expand Up @@ -39,7 +39,7 @@ Sample preparation and metabolite extraction:
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).

# Get Help
## Get Help
If you have any further questions about the management and analysis of your microbial research data, please contact us: [[email protected]](mailto:[email protected]) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/))

## References
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2 changes: 1 addition & 1 deletion ...rimental-Procedure-Standards-SOPs/07-metabolite-extraction-from-plant-tissue.md
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Expand Up @@ -35,7 +35,7 @@ h. Collect sample eluent and evaporate the samples to dryness in a SpeedVac conc

7. Sample are reconstituted in mobile phase (or 50% methanol) before analysis

# Get Help
## Get Help
If you have any further questions about the management and analysis of your microbial research data, please contact us: [[email protected]](mailto:[email protected]) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/))

## References
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2 changes: 1 addition & 1 deletion ..._Experimental-Procedure-Standards-SOPs/08-proteomics-tmt-labelled-sp3-method.md
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Expand Up @@ -100,7 +100,7 @@ Sample elution & collection:
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

# Get Help
## Get Help
If you have any further questions about the management and analysis of your microbial research data, please contact us: [[email protected]](mailto:[email protected]) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/))

## References
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8 changes: 4 additions & 4 deletions ...rimental-Procedure-Standards-SOPs/09-sample-collection-and-storage-by-sample.md
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Expand Up @@ -13,8 +13,8 @@ Protein storage at -20°C usually requires the addition of 50% glycerol to your
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.


| Sample | Procedure | Source or Link |
|----------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------|
| Sample | Procedure | Source or Link |
|---------|------------|-----------------|
| Activated sludge from wastewater | 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 | {% cite Morin_2020 %} |
| Antarctic ticks | collected from rocks, placed in RNALater and stored at -80°C within 4-8 h of collection | {% cite Wille_2020 %} |
| Atlantic salmon | dissection samples placed in RNAlater and stored at -80°C | {% cite Karlsen_2022 %} |
Expand Down Expand Up @@ -43,9 +43,9 @@ Protein samples stored at -80ºC will be frozen. As repeated freeze-thaw cycles
| Turkey Trachea swabs | placed in 1 ml PBS, then stored at -20°C | {% cite Kursa_2021 %} |
| Vaginal swabs | 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). | (in-house protocol provided by Pamela Ferretti) |
| Yoghurt | after purchase, samples were placed immediately at 4°C for transport and within 12 h stared at -80°C | {% cite Islam_2021 %} |
{: .table .table-hover}


# Get Help
## Get Help
If you have any further questions about the management and analysis of your microbial research data, please contact us: [[email protected]](mailto:[email protected]) (by emailing us you agree to the privacy policy on our website: [Contact](https://nfdi4microbiota.de/contact-form/))

## References
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2 changes: 2 additions & 0 deletions docs/_Getting-Started/01-privacy-policy-english-translation.md
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The following policy is an automated translation of the German text. Please refer to the German original for a legally binding document.

---

## § 1 Information on data collection, controller, contacting us


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20 changes: 15 additions & 5 deletions docs/_Getting-Started/02-contributing.md
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Expand Up @@ -16,13 +16,17 @@ The main steps a user must follow to contribute to the Knowledge Base are:
2. Make changes to files in the repository:
- Edit existing files *or*
- Create new files
3. Add your name to the [03-contributors.md](https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base/blob/main/docs/_Getting-Started/03-contributors.md) file
3. Add your name to the [03-contributors.md](https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base/blob/main/docs/_Getting-Started/03-contributors.md) file.

---

## Create a GitHub account


Users will need a GitHub account if they wish to contribute to the Knowledge Base. If you do not already have an account, go to the GitHub [homepage](https://github.com/) and click the `Sign Up` button to create one. Then follow the instructions. Once you have created an account, and signed in, go to the [Knowledge Base repository](https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base.github.io)

---

## Make changes to the repository


Expand Down Expand Up @@ -67,11 +71,14 @@ To create a new issue:

[Here](https://docs.github.com/en/issues/tracking-your-work-with-issues/creating-an-issue) is a guide on creating issues on GitHub if you need further help.

---

## Add your name to the CONTRIBUTORS file


We appreciate your contribution! Please add your name to the [03-contributors.md](https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base/blob/main/docs/_Getting-Started/03-contributors.md) file.

---

## Contribution Rules

Expand All @@ -82,13 +89,16 @@ When adding or editing files, please observe the following rules:
2. Use American English
3. Keep the content factual
4. Reference sources appropriately (see below)
5. Use a single `#` for the main file heading and use `##`, `###`, etc, for all subheadings
6. Place image files in the `assets/img/` directory
7. Use internal links to markdown documents with {% raw %}`[Link text]({% link _RDM-Share/26_licenses.md %})`{% endraw %}
8. Non-public links are be restricted to the how-we-operate section and whitelisted in `.github/workflows/ignored-urls.txt` manually
5. Use a single `##` for the main file heading and use `###`, `####`, etc, for all subheadings
6. Before the second and every following `##` add `---` for a visual break line.
7. Place image files in the `assets/img/` directory
8. Use internal links to markdown documents with {% raw %}`[Link text]({% link _RDM-Share/26_licenses.md %})`{% endraw %}
9. Non-public links are be restricted to the how-we-operate section and whitelisted in `.github/workflows/ignored-urls.txt` manually

*Note: we might edit your contribution to homogenize the writing style.*

---

## Cite sources


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