From 7be4314fe65e651562401f735942613dfdc367e7 Mon Sep 17 00:00:00 2001
From: Mekhrona Mirzoeva <memir101@hhu.de>
Date: Thu, 20 Mar 2025 16:20:48 +0100
Subject: [PATCH] 16S profiling analysis

---
 .gitattributes                                  |   2 ++
 assays/Analysis of 16S profiling/README.md      |   0
 .../Analysis of 16S profiling/dataset/.gitkeep  |   0
 .../dataset/ComProfiling.jpg                    |   3 +++
 assays/Analysis of 16S profiling/isa.assay.xlsx | Bin 0 -> 11322 bytes
 .../protocols/.gitkeep                          |   0
 .../protocols/16SProfilingAnalysis.md           |  12 ++++++++++++
 7 files changed, 17 insertions(+)
 create mode 100644 assays/Analysis of 16S profiling/README.md
 create mode 100644 assays/Analysis of 16S profiling/dataset/.gitkeep
 create mode 100644 assays/Analysis of 16S profiling/dataset/ComProfiling.jpg
 create mode 100644 assays/Analysis of 16S profiling/isa.assay.xlsx
 create mode 100644 assays/Analysis of 16S profiling/protocols/.gitkeep
 create mode 100644 assays/Analysis of 16S profiling/protocols/16SProfilingAnalysis.md

diff --git a/.gitattributes b/.gitattributes
index 4b96006..7bc447f 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -15,3 +15,5 @@ assays/MicrobiotaReconstitutionFlowpot/dataset/.gitkeep filter=lfs diff=lfs merg
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 assays/DNA[[:space:]]Isolation/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text
 assays/Library[[:space:]]preparation[[:space:]]for[[:space:]]bacterial[[:space:]]16S[[:space:]]rRNA[[:space:]]gene[[:space:]]profiling/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text
+assays/Analysis[[:space:]]of[[:space:]]16S[[:space:]]profiling/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text
+assays/Analysis[[:space:]]of[[:space:]]16S[[:space:]]profiling/dataset/ComProfiling.jpg filter=lfs diff=lfs merge=lfs -text
diff --git a/assays/Analysis of 16S profiling/README.md b/assays/Analysis of 16S profiling/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/assays/Analysis of 16S profiling/dataset/.gitkeep b/assays/Analysis of 16S profiling/dataset/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/Analysis of 16S profiling/dataset/ComProfiling.jpg b/assays/Analysis of 16S profiling/dataset/ComProfiling.jpg
new file mode 100644
index 0000000..dad107f
--- /dev/null
+++ b/assays/Analysis of 16S profiling/dataset/ComProfiling.jpg	
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diff --git a/assays/Analysis of 16S profiling/protocols/.gitkeep b/assays/Analysis of 16S profiling/protocols/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/assays/Analysis of 16S profiling/protocols/16SProfilingAnalysis.md b/assays/Analysis of 16S profiling/protocols/16SProfilingAnalysis.md
new file mode 100644
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+++ b/assays/Analysis of 16S profiling/protocols/16SProfilingAnalysis.md	
@@ -0,0 +1,12 @@
+## Analysis of 16S profiling data
+
+### ASV table generation
+
+Amplicon sequencing reads from *A. thaliana* roots and Flowpot soil were quality filtered and demultiplexed according to their barcode sequence using QIIME (26) and unique amplicon sequencing variants (ASVs) were inferred from error-corrected reads, followed by chimera filtering. ASVs were mapped to the reference 16S rRNA sequences (downloaded from “www.at-sphere.com”) to generate an ASV count table. All steps were carried out using the Rbec R package (27). Analysis was performed on samples with a sequencing depth of at least 500 high-quality reads.
+
+
+### Alpha- and beta-diversity
+
+Analyses and visualization were performed in the R statistical environment (Version 4.1.2).
+Alpha and beta diversity were calculated on non-rarefied ASV count tables (28). Alpha-diversity (Shannon index) was calculated with the “plot_richness” function in phyloseq package (29).
+Beta-diversity (Bray-Curtis dissimilarities) was calculated using the “ordinate” function in phyloseq package and used for unconstrained ordination by Principal Coordinate Analysis (PCoA). Statistical significances were assessed using permutational multi-variate analysis of variance (PERMANOVA) using the adonis function in the vegan package.
-- 
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