diff --git a/assays/Talinum_RNASeq_minimal/isa.assay.xlsx b/assays/Talinum_RNASeq_minimal/isa.assay.xlsx index 1ee1a4f320dc00b3b7d292242fae5321305e2157..2305b3f43257233eed2ed2a03142f9a8f23d90f9 100644 Binary files a/assays/Talinum_RNASeq_minimal/isa.assay.xlsx and b/assays/Talinum_RNASeq_minimal/isa.assay.xlsx differ diff --git a/assays/Talinum_RNASeq_minimal/protocols/RNAex_libraries.md b/assays/Talinum_RNASeq_minimal/protocols/RNAex_libraries.md deleted file mode 100644 index 6f0d1cdb16e0a75ff73bd0aa530584e5a47d53f2..0000000000000000000000000000000000000000 --- a/assays/Talinum_RNASeq_minimal/protocols/RNAex_libraries.md +++ /dev/null @@ -1,10 +0,0 @@ -``` -Note: -- This is a somewhat polished protocol as found in a publication. -- This is not an example for a typical lab protocol or method. -``` - - -# RNA Extraction, Preparation, and Sequencing of Illumina Libraries - -The topmost mature unshaded leaves (of approximately 3–4.5 cm length) of *T. triangulare* were harvested in the middle of the light or the middle of the dark period and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the GeneMatrix Universal RNA Purification Kit (EURx Ltd.). Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library, and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) and quantified with a Qubit 2.0 (Invitrogen). Samples were multiplexed with 12 libraries per lane and sequenced in single-end mode (Rapid Run, 150 bp read length) on an Illumina HiSeq 2000 platform. diff --git a/assays/Talinum_RNASeq_minimal/protocols/illumina.md b/assays/Talinum_RNASeq_minimal/protocols/illumina.md new file mode 100644 index 0000000000000000000000000000000000000000..fecf1eb717e733b86973299a71f6d3a22811505b --- /dev/null +++ b/assays/Talinum_RNASeq_minimal/protocols/illumina.md @@ -0,0 +1,3 @@ +# Preparation and Sequencing of Illumina Libraries + +RNA integrity, sequencing library, and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) and quantified with a Qubit 2.0 (Invitrogen). Samples were multiplexed with 12 libraries per lane and sequenced in single-end mode (Rapid Run, 150 bp read length) on an Illumina HiSeq 2000 platform. diff --git a/assays/Talinum_RNASeq_minimal/protocols/rna_extraction.md b/assays/Talinum_RNASeq_minimal/protocols/rna_extraction.md new file mode 100644 index 0000000000000000000000000000000000000000..4a87be713f40d4c91fff21ad3becf8a2b657cffe --- /dev/null +++ b/assays/Talinum_RNASeq_minimal/protocols/rna_extraction.md @@ -0,0 +1,3 @@ +# RNA Extraction + +RNA was isolated from ground tissue using the GeneMatrix Universal RNA Purification Kit (EURx Ltd.). Residues of DNA were removed with DNase (New England Biolabs). \ No newline at end of file diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index 06049c1cae9e0f1431580e8babf7cdd97d6ac8eb..5568470d34cd2f4344f4bdab2194e2c62593b9bb 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/studies/TalinumFacultativeCAM/isa.study.xlsx b/studies/TalinumFacultativeCAM/isa.study.xlsx index 9626ca8dbb0a9077075e18bf3cd07b9440da2b53..2b5d5bbefa04909d9f4791ad9db51f14bb830c14 100644 Binary files a/studies/TalinumFacultativeCAM/isa.study.xlsx and b/studies/TalinumFacultativeCAM/isa.study.xlsx differ diff --git a/studies/TalinumFacultativeCAM/protocols/.gitkeep b/studies/TalinumFacultativeCAM/protocols/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/studies/TalinumFacultativeCAM/protocols/plant_material.md b/studies/TalinumFacultativeCAM/protocols/plant_material.md index 0c03bf77b9182231094098c2b5d124f5ba8b0788..6b81fa2e22dd13fdafda15edd57d9c08f4883136 100644 --- a/studies/TalinumFacultativeCAM/protocols/plant_material.md +++ b/studies/TalinumFacultativeCAM/protocols/plant_material.md @@ -1,9 +1,8 @@ -``` -Note: -- This is a somewhat polished protocol as found in a publication. -- This is not an example for a typical lab protocol or method. -``` - # Plant Material and Growth Conditions -*Talinum triangulare* plants were grown in Miracle-Gro Potting Mix (Miracle-Gro) in “Short-One†treepots, 1.6 l (Stuewe and Sons). The experiment was initiated with 28-d-old plants in a controlled environment chamber (Environmental Growth Chambers) maintained under 12 h light (30°C, 37% relative humidity)/12 h dark (22°C) cycles. Photon flux density at leaf level was 425 mmol m<sup>-2</sup> s<sup>-1</sup>. Irrigation was withheld on day 1 and recommenced on day 14. Leaves were harvested when plants were well-watered as well as after 4, 9, and 12 days of water deprivation and watered for two days following the drought period. \ No newline at end of file +*Talinum triangulare* plants were grown in Miracle-Gro Potting Mix (Miracle-Gro) in “Short-One†treepots, 1.6 l (Stuewe and Sons). The experiment was initiated with 28-d-old plants in a controlled environment chamber (Environmental Growth Chambers) maintained under 12 h light (30°C, 37% relative humidity)/12 h dark (22°C) cycles. Photon flux density at leaf level was 425 mmol m<sup>-2</sup> s<sup>-1</sup>. + + +# Treatment and harvest + +Irrigation was withheld on day 1 and recommenced on day 14. Leaves were harvested when plants were well-watered as well as after 4, 9, and 12 days of water deprivation and watered for two days following the drought period. The topmost mature unshaded leaves (of approximately 3–4.5 cm length) of *T. triangulare* were harvested in the middle of the light or the middle of the dark period and immediately frozen in liquid nitrogen. diff --git a/studies/TalinumFacultativeCAM/resources/.gitkeep b/studies/TalinumFacultativeCAM/resources/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/studies/TalinumGenomeDraft/isa.study.xlsx b/studies/TalinumGenomeDraft/isa.study.xlsx index a12118f2e0c76cb2611156271ad11f47f1bd6a25..55fe82418c3e71f0a6102613ee16fd366c071c21 100644 Binary files a/studies/TalinumGenomeDraft/isa.study.xlsx and b/studies/TalinumGenomeDraft/isa.study.xlsx differ diff --git a/studies/TalinumGenomeDraft/resources/.gitkeep b/studies/TalinumGenomeDraft/resources/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000