diff --git a/assays/CMML_16-0016_GCMS/protocols/.gitkeep b/assays/CMML_16-0016_GCMS/protocols/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/assays/CMML_16-0016_GCMS/protocols/Probenliste_Sladjana.xlsx b/assays/CMML_16-0016_GCMS/protocols/Probenliste_Sladjana.xlsx deleted file mode 100755 index 1d3e7706fbb7a5f116081724b60baf5100d9e1e2..0000000000000000000000000000000000000000 Binary files a/assays/CMML_16-0016_GCMS/protocols/Probenliste_Sladjana.xlsx and /dev/null differ diff --git a/assays/rna-data-processing/protocols/.gitkeep b/assays/rna-data-processing/protocols/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/assays/rna-seq/dataset/.gitkeep b/assays/rna-seq/dataset/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/assays/rna-seq/isa.assay.xlsx b/assays/rna-seq/isa.assay.xlsx index c2e11361091f4b2c35bba447ab4203d41d334853..ca54f1231e4f60e72afed0f8839f46b985d5d3a1 100644 Binary files a/assays/rna-seq/isa.assay.xlsx and b/assays/rna-seq/isa.assay.xlsx differ diff --git a/assays/rna-seq/protocols/.gitkeep b/assays/rna-seq/protocols/.gitkeep deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/assays/rna-seq/protocols/GSE86380_MetaData.xls b/assays/rna-seq/protocols/GSE86380_MetaData.xls index 340e2704ffb5776b2e6be6b2e2e930a49f03f044..b858519cf1b45348cf5fc8601bc77e567f366829 100644 Binary files a/assays/rna-seq/protocols/GSE86380_MetaData.xls and b/assays/rna-seq/protocols/GSE86380_MetaData.xls differ diff --git a/assays/rna-seq/protocols/extract protocol.md b/assays/rna-seq/protocols/extract protocol.md deleted file mode 100644 index d6faefe05fb4835a05b2d40da1ebb639fc5cfefe..0000000000000000000000000000000000000000 --- a/assays/rna-seq/protocols/extract protocol.md +++ /dev/null @@ -1 +0,0 @@ -Mature leaves were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the Qiagen RNeasy plant mini kit. 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). diff --git a/assays/rna-seq/protocols/illumina-libraries.md b/assays/rna-seq/protocols/illumina-libraries.md new file mode 100644 index 0000000000000000000000000000000000000000..84715754c1078775dae4ea2c1ad71adef7eb1230 --- /dev/null +++ b/assays/rna-seq/protocols/illumina-libraries.md @@ -0,0 +1,3 @@ +# Preparation and Sequencing of Illumina Libraries + + Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego,CA, United States) and quantified with a Qubit 2.0 (Invitrogen, Waltham, MA, United States). Samples were multiplexed with 12 libraries per lane and sequenced in paired-end mode (Rapid Run, 150 bp read length) on an Illumina HiSeq 3000 platform, yielding on average ∼26 million reads per library. diff --git a/assays/rna-seq/protocols/library construction protocol.md b/assays/rna-seq/protocols/library construction protocol.md deleted file mode 100644 index 6e15b0d8fbcb7a0de6523066dfc0e7ce1e1b26f0..0000000000000000000000000000000000000000 --- a/assays/rna-seq/protocols/library construction protocol.md +++ /dev/null @@ -1 +0,0 @@ -Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in paired-end mode (150 bp read length) on an Illumina HiSeq 3000 platform. diff --git a/assays/rna-seq/protocols/rna-extraction.md b/assays/rna-seq/protocols/rna-extraction.md new file mode 100644 index 0000000000000000000000000000000000000000..efda017a3febecb3fd5193488da2003ea18b98f5 --- /dev/null +++ b/assays/rna-seq/protocols/rna-extraction.md @@ -0,0 +1,3 @@ +# RNA Extraction + +Whole rosettes were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the RNeasyPlant Mini Kit (QIAGEN, Hilden, Germany). Residues of DNAwere removed with DNase (New England Biolabs, Ipswitch, MA,United States). RNA integrity, sequencing library, and fragment size were analyzed on a 2100 Bioanalyzer (Agilent Technologies,Santa Clara, CA, United States).