Identifying lncRNAs in I. sinensis

Total RNA was extracted from each I. sinensis sample using the RNeasy Plus Mini Kit, and rRNA removal was performed using a RiBO-Zero Kit. Isolated RNA was used for cDNA library construction, using the dUTP method [74 (link)]. These libraries were sequenced on an Illumina HiSeq X Ten platform. The purity, concentration, and integrity of RNA were checked using the agarose gel electrophoresis, the Qubit 2.0 Fluorometer, and the Agilent 4150 TapeStation, respectively. After trimming adapters and filtering out low-quality reads, a total of 14.02 Gb clean reads were generated. The transcriptome was mapped to the reference genome using TopHat2 [75 (link)]. Transcripts greater than 200 bp in length and containing at least 2 exons were considered lncRNA candidates. Four computational approaches, including CPC [76 (link)], CNCI [77 (link)], Pfam (RRID:SCR_004726), and PhyloCSF [78 (link)], were combined to evaluate the protein-coding capability of the lncRNA candidates.

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Cui J., Zhu Y., Du H., Liu Z., Shen S., Wang T., Cui W., Zhang R., Jiang S., Wu Y., Gu X., Yu H, & Liang Z. (2023). Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes. GigaScience, 12, giad079.

Publication 2023

HiSeq X Ten 2.0 Fluorometer 4150 TapeStation

Agarose gel electrophoresis Cdna library Dutp Exons Lncrna Protein Rrna Transcriptome

Corresponding Organization : Biotechnology Research Institute

Other organizations : Beijing University of Agriculture, Southwest University, Beijing Academy of Agricultural and Forestry Sciences, BGI Group (China), National University of Singapore

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Transcriptome assembly and characterization of long non-coding RNAs (lncRNAs) in I. sinensis

control variables

None explicitly mentioned

controls

Positive control: None mentioned
Negative control: None mentioned

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