diff --git a/.gitattributes b/.gitattributes index e09f5624751fd10effd96d81a926b8450b4a3f6f..eac08543a6914931ee21efdfcfd9a63f1c82b702 100644 --- a/.gitattributes +++ b/.gitattributes @@ -13,3 +13,4 @@ assays/InvitroIronMobilizationAssay/dataset/.gitkeep filter=lfs diff=lfs merge=l assays/BacterialGrowthRates/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text assays/MicrobiotaReconstitutionFlowpot/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text assays/Mono-association[[:space:]]experiment[[:space:]]of[[:space:]]R401[[:space:]]on[[:space:]]Athaliana[[:space:]]seedlings[[:space:]]in[[:space:]]agar[[:space:]]plates/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text +assays/DNA[[:space:]]Isolation/dataset/.gitkeep filter=lfs diff=lfs merge=lfs -text diff --git a/assays/DNA Isolation/README.md b/assays/DNA Isolation/README.md new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/DNA Isolation/dataset/.gitkeep b/assays/DNA Isolation/dataset/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/DNA Isolation/isa.assay.xlsx b/assays/DNA Isolation/isa.assay.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..ddc862f7661c2d0a140f7b43b1c18ba3955a4a21 Binary files /dev/null and b/assays/DNA Isolation/isa.assay.xlsx differ diff --git a/assays/DNA Isolation/protocols/.gitkeep b/assays/DNA Isolation/protocols/.gitkeep new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/assays/DNA Isolation/protocols/DNAIsolation.md b/assays/DNA Isolation/protocols/DNAIsolation.md new file mode 100644 index 0000000000000000000000000000000000000000..abb6f076aa7381ea83ca84a88a8dddb7a5940ab0 --- /dev/null +++ b/assays/DNA Isolation/protocols/DNAIsolation.md @@ -0,0 +1,4 @@ +## DNA isolation + +For DNA extractions, root and soil samples were homogenized in a Precellys 24 TissueLyser (Bertin Technologies) for 2 x 30 s at 6,200 rpm with 15 s intervals. DNA was extracted with a modified, high-throughput version of the FastDNA SPIN kit for Soil (MP Biomedicals). In brief, samples were taken up in sodium phosphate buffer (MP Biomedicals) and MT buffer (MP Biomedicals), then homogenized as described before. +After centrifugation for 15 min at 13,000 rpm, 150 μl of the supernatant were transferred to a 96-well Acroprep Advance filter plate (with 0.2 μm Supor filter; Pall). Once full, the filter plate was positioned on a PCR plate filled with 50 μl Binding Matrix (MP Biomedicals) per well and centrifuged for 15 min to remove residual soil particles. This and all subsequent centrifugation steps were carried out in a swing out centrifuge at 1,500 rpm. The PCR plate was sealed and shaken for 3 min to allow binding of the DNA to the Binding Matrix. The suspension was pipetted onto a second filter plate of the same kind, positioned on a collection plate, and centrifuged for 15 min. The flowthrough was discarded. Then, 200 μl SEWS-M washing buffer (MP Biomedicals) were pipetted into each well of the filter plate and centrifuged for 5 min. This washing step was carried out a second time. The flowthrough was discarded and followed by centrifugation for 5 min to remove residual SEWS-M buffer. Finally, 30 μl nuclease-free water were added to each well and left to incubate at room temperature for 3 min. Subsequent centrifugation for 5 min eluted the DNA into a clean PCR plate. The resulting DNA was used for v5v7 16S rRNA region amplification without prior adjustment of DNA concentrations. \ No newline at end of file diff --git a/assays/Mono-association experiment of R401 on Athaliana seedlings in agar plates/isa.assay.xlsx b/assays/Mono-association experiment of R401 on Athaliana seedlings in agar plates/isa.assay.xlsx index b39051ed2ff6a840d08b1ddca5f9605cc830054c..ec9fa726e86867886f3b6fc1d5ede9d5f42d2d70 100644 Binary files a/assays/Mono-association experiment of R401 on Athaliana seedlings in agar plates/isa.assay.xlsx and b/assays/Mono-association experiment of R401 on Athaliana seedlings in agar plates/isa.assay.xlsx differ