diff --git a/assays/RNASeq_drought/isa.assay.xlsx b/assays/RNASeq_drought/isa.assay.xlsx index 34091770017d4c200ac3b725712e7794b15870ac..692975322939af3a28c2354584238472573f4fb0 100644 Binary files a/assays/RNASeq_drought/isa.assay.xlsx and b/assays/RNASeq_drought/isa.assay.xlsx differ diff --git a/assays/RNASeq_drought/protocols/cDNA_library_construction_and_sequencing.docx b/assays/RNASeq_drought/protocols/cDNA_library_construction_and_sequencing.docx new file mode 100644 index 0000000000000000000000000000000000000000..19757ad8122b7c78b903311a6547a2497e84112c Binary files /dev/null and b/assays/RNASeq_drought/protocols/cDNA_library_construction_and_sequencing.docx differ diff --git a/assays/Ribes_nigrum_genome_sequencing/README.md b/assays/Ribes_nigrum_genome_sequencing/README.md index 38c14e1fb355ceea1abe6d96f1d9968c9d426d4f..d837a762d0b56a4c22a82e17bbf9ecfa92406792 100644 --- a/assays/Ribes_nigrum_genome_sequencing/README.md +++ b/assays/Ribes_nigrum_genome_sequencing/README.md @@ -1,4 +1,4 @@ # Genome sequencing -For generating a *Ribes nigrum* genome assembly, the cultivar Rosenthals Langtraubige was used. DNA was extracted and filtered for long fragments above 40 kbp in order to perform Oxformd Nanopore (ONT) sequencing and PacBio sequencing. +For generating a *Ribes nigrum* genome assembly, the cultivar Rosenthals Langtraubige was used. DNA was extracted and filtered for long fragments above 40 kbp in order to perform Oxford Nanopore (ONT) sequencing and PacBio sequencing. Briefly, DNA was extracted, short fragments filtered out, DNA purity confirmed, and the libraries were prepared using the standard ONT protocol for the SQK-LSK112 kit. After DNA fragment repair and 3'-adenylation sequencing adapters were ligated to the DNA fragments, before a last purification step with AMPure XP beads. ONT sequencing was performed in-house, PacBio sequencing was performed by Genohub (Brigham Young University, Provo, UT, USA). \ No newline at end of file diff --git a/studies/Ribes_nigrum_genome/resources/Russell2011.pdf b/studies/Ribes_nigrum_genome/resources/Russell2011.pdf new file mode 100644 index 0000000000000000000000000000000000000000..d21b5c9bf43fc76d98b900591ecad8d3aba80d91 Binary files /dev/null and b/studies/Ribes_nigrum_genome/resources/Russell2011.pdf differ diff --git a/studies/Ribes_nigrum_transcriptome/README.md b/studies/Ribes_nigrum_transcriptome/README.md index c1e6abc633f5b3879c60594abb49a997f73ec42d..58edb508fc238ea22714f419de246a9444cd8118 100644 --- a/studies/Ribes_nigrum_transcriptome/README.md +++ b/studies/Ribes_nigrum_transcriptome/README.md @@ -1,10 +1,11 @@ # Drought stress experiment -A greenhouse experiment was performed to investigate the influence of drought stress on the gene expression of *R. nigrum* cv Rosenthals Langtraubige. Stressed plants that were not watered for 4 days were compared to control plants with continuous irrigation. Both leaves and roots were sampled for RNA extraction. +A greenhouse experiment was performed to investigate the influence of drought stress on the gene expression of *R. nigrum* cv Rosenthals Langtraubige. Stressed plants (A-C) that were not watered for 4 days were compared to control plants (D-F) with continuous irrigation. Both leaves and roots were sampled for RNA extraction. +<img src="./protocols/greenhouse_drought_experiment.png" width="600"> + - Figure from [Ziegler et al. 2024](https://doi.org/10.1093/hr/uhae313) \ No newline at end of file diff --git a/studies/Ribes_nigrum_transcriptome/isa.study.xlsx b/studies/Ribes_nigrum_transcriptome/isa.study.xlsx index 5a10514c6c8ddf7311b92b634f34d8bcf4a53dd7..923350861df5607bf950f746e8b8332c9570a479 100644 Binary files a/studies/Ribes_nigrum_transcriptome/isa.study.xlsx and b/studies/Ribes_nigrum_transcriptome/isa.study.xlsx differ diff --git a/studies/Ribes_nigrum_transcriptome/protocols/Drought_experiment.docx b/studies/Ribes_nigrum_transcriptome/protocols/Drought_experiment.docx new file mode 100644 index 0000000000000000000000000000000000000000..9d17c27392cb397caeafdd4247e0aa94843c519e Binary files /dev/null and b/studies/Ribes_nigrum_transcriptome/protocols/Drought_experiment.docx differ