Transcriptome Analysis of Plant Leaf Samples

Fresh young leaf samples were frozen on dry ice in the field and stored at − 80 °C until total RNA extraction. Preliminary RNA precipitation [29 (link), 30 (link)] as performed prior to total RNA extraction with the Qiagen RNeasy Plant Mini Kit protocol with DNase treatment (Qiagen, Hilden, Germany). RNA-Seq libraries with insert length 100–380 bp (mode = 170 bp) were prepared from 4 μg of RNA using an Illumina TruSeq RNA Sample Prep Kit. Each library was uniquely tagged using 12 TruSeq indexed adapters (numbers 1–12) to enable 12-plexing of samples in each Illumina HiSeq 2000 lane.

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Oney-Birol S., Fitz-Gibbon S., Chen J.M., Gugger P.F, & Sork V.L. (2018). Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus). BMC Genetics, 19, 88.

Publication 2018

RNeasy Plant Mini Kit TruSeq RNA Sample Prep Kit HiSeq 2000 lane

Bp 100 Dnase Dry ice Frozen Leaf Library Plant Protocol treatment Rna seq

Corresponding Organization : Burdur Mehmet Akif Ersoy Üniversitesi

Other organizations : University of California, Los Angeles, Chinese Academy of Sciences, Wuhan Botanical Garden

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Variable analysis

independent variables

Fresh young leaf samples
RNA precipitation prior to extraction

dependent variables

Total RNA extraction
RNA-Seq library preparation
Insert length 100–380 bp (mode = 170 bp)

control variables

Freezing of leaf samples on dry ice in the field
Storage of samples at − 80 °C until RNA extraction
DNase treatment during RNA extraction with Qiagen RNeasy Plant Mini Kit protocol
Use of 4 μg of RNA for RNA-Seq library preparation
12-plexing of samples in each Illumina HiSeq 2000 lane

positive controls

None specified

negative controls

None specified

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