From a2a1cbb346cf5bbe9447f35eb2ff89c18c773c3b Mon Sep 17 00:00:00 2001
From: Viktoria Petrova <vipet103@hhu.de>
Date: Tue, 26 Nov 2024 17:34:28 +0100
Subject: [PATCH] create accession selection study and protocol

---
 studies/AccessionSelection/README.md             |   0
 studies/AccessionSelection/isa.study.xlsx        | Bin 0 -> 7495 bytes
 studies/AccessionSelection/protocols/.gitkeep    |   0
 .../protocols/AccessionSelectionProtocol.md      |   3 +++
 studies/AccessionSelection/resources/.gitkeep    |   0
 5 files changed, 3 insertions(+)
 create mode 100644 studies/AccessionSelection/README.md
 create mode 100644 studies/AccessionSelection/isa.study.xlsx
 create mode 100644 studies/AccessionSelection/protocols/.gitkeep
 create mode 100644 studies/AccessionSelection/protocols/AccessionSelectionProtocol.md
 create mode 100644 studies/AccessionSelection/resources/.gitkeep

diff --git a/studies/AccessionSelection/README.md b/studies/AccessionSelection/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/studies/AccessionSelection/isa.study.xlsx b/studies/AccessionSelection/isa.study.xlsx
new file mode 100644
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diff --git a/studies/AccessionSelection/protocols/.gitkeep b/studies/AccessionSelection/protocols/.gitkeep
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diff --git a/studies/AccessionSelection/protocols/AccessionSelectionProtocol.md b/studies/AccessionSelection/protocols/AccessionSelectionProtocol.md
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+## Accession selection
+
+In order to establish clusters of *A. thaliana* accessions with high versus low S content in their leaves, we re-analyzed ionomics data from Baxter et al. (2007) and Campos et al. (2021), with 174 accessions overlapping in the two datasets (Baxter et al., 2007; Campos et al., 2021). The two datasets of Baxter et al. (2007) and Campos et al. (2021) have different ranges of S concentrations, and individual accessions differ in absolute value but are usually in a similar percentile or relative range, with some exceptions. Therefore, we aimed to use only the overlapping accessions and to use both datasets to decide which accessions to choose. From these 174 overlapping accessions, a principal component analysis (PCA) was performed on the total of 37 ion data (Supplementary Table S1) to establish groupings of accessions with similar leaf S content. Based on the availability of these accessions, we selected 20 accessions with low, medium, and high sulfate levels for further investigation (Supplementary Fig. S1; Supplementary Table S1).
\ No newline at end of file
diff --git a/studies/AccessionSelection/resources/.gitkeep b/studies/AccessionSelection/resources/.gitkeep
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-- 
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