Maize Transcriptome Profiling via Iso-Seq

Total RNA was extracted from leaf, stem, silk, husk, ear and pollen tissues using Trizol and RNeasy MinElute (Qiagen) RNA clean up kit, with an Dnase I treatment of 20 min^{69 (link)}. The RNA integrity was assessed with a Bioanalyzer prior to the construction of the Iso-Seq library. The Iso-Seq libraries were prepared and sequenced by Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida using a PacBio Sequel system. PacBio Iso-Seq data were analyzed by running the IsoSeq3 v3.1 in PacBio SMART Analysis v7.0 (https://github.com/PacificBiosciences/IsoSeq3) to generate high-quality, full-length transcript sequences.

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Hu Y., Colantonio V., Müller B.S., Leach K.A., Nanni A., Finegan C., Wang B., Baseggio M., Newton C.J., Juhl E.M., Hislop L., Gonzalez J.M., Rios E.F., Hannah L.C., Swarts K., Gore M.A., Hennen-Bierwagen T.A., Myers A.M., Settles A.M., Tracy W.F, & Resende MF J.r. (2021). Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Nature Communications, 12, 1227.

Publication 2021

RNeasy MinElute

Dnase i Leaf Library Pollen Silk Stem Tissues Trizol

Corresponding Organization :

Other organizations : University of Florida, Cold Spring Harbor Laboratory, Cornell University, Iowa State University, University of Wisconsin–Madison, Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences

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Variable analysis

independent variables

Tissue type (leaf, stem, silk, husk, ear, pollen)

dependent variables

RNA integrity
Full-length transcript sequences

control variables

RNA extraction method (Trizol and RNeasy MinElute)
DNase I treatment duration (20 min)

controls

Positive control: Not specified
Negative control: Not specified

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