The plant material used in this study was collected from M. ternifolia plants cultivated in the Yunnan province of China. The developing fruit kernels comprised of young (S1), medium-aged (S2), and mature (S3) fruiting stages were picked in three biological repeats. The harvested samples were immediately placed in liquid nitrogen and stored at −80 °C before further processing. Total RNA was isolated from all nine samples with a Trizol reagent (Invitrogen, San Diego, CA, USA) following the manufacturer’s standard protocol. RNase-free DNase I (TaKaRa, Kyoto, Japan) was used to purify the total RNA. The RNA quality and quantity were determined by 1% agarose gel and Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA), respectively. Sequencing libraries were prepared with the Illumina TruSeq Standard mRNA library preparation kit following the manufacturer’s standard protocol. After the quality tests, the Illumina HiSeq Ten X platform (Illumina Inc., San Diego, CA, USA) was used according to the recommended protocol to perform de novo pair-end RNA sequencing.
Truseq standard mrna library preparation kit
Manufactured by Illumina
The TruSeq Standard mRNA library preparation kit is a product designed to prepare mRNA samples for sequencing. It provides the necessary reagents and protocols to extract and purify mRNA from total RNA samples, and to generate sequencing-ready libraries from the purified mRNA.
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Lab products found in correlation
2 protocols using truseq standard mrna library preparation kit
1
Transcriptome Profiling of M. ternifolia Fruit Development
2
RNA-seq Library Preparation and Sequencing
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RNA-seq libraries were prepared using the TruSeq standard mRNA library preparation kit [for poly(A)-RNA-seq; Illumina] or the ovation universal RNA-seq system (for rRNA-depleted RNA-seq; NuGEN) and sequenced by the HiSeq 2500 sequencing system (Illumina). Note that except for the results shown in Supplemental Figure S1, D–F , all of our analyses were performed on poly(A)-selected libraries. This choice was made to minimize the number of falsely identified non-XDT genes: Poly(A)-selected libraries contained fewer sporadic intergenic reads than rRNA-depleted libraries in wild-type (XRN2-proficient) conditions. Since readthrough is defined via a comparison between xrn-2-depleted and control conditions, this lower background permitted more facile detection of readthrough (i.e., XDT genes) and thus helped to avoid false-positive identifications of non-XDT genes.
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