Generation of transcriptional novelty by transposable element insertions in Arabidopsis, Genome Sequencing and eccDNA Data
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<strong>Raw Illumina sequencing data from the Manuscript entitled "Generation of transcriptional novelty by transposable element insertions in Arabidopsis"</strong> <strong>A. Illumina genome sequencing reads of Arabidopsis control and hcLines that contain novel transposable element insertions.</strong> To identify the genomic position of the new <em>ONSEN</em> insertions, the extracted DNA of the 11 selected lines (nine lines with new insertions and two control lines) was sent to BGI, Hong-Kong for Illumina paired-end 150 bp sequencing, aiming for a minimum of 20X sequencing coverage. Quality control of the raw reads was done using FastQC (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and trimming/clipping was done using Trimmomatic with parameters ILLUMINACLIP: TruSeq3:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 and MINLEN:36. Quality of the reads was deemed excellent and no further actions were taken. Samples identifications: genome_hcLineX with "_1" indicating the forward and "_2" the reverse reads. <strong>B. Illumina eccDNA sequencing of Arabidopsis control and hcLines following stress treatments</strong> Extrachromosomal circular DNA was prepared and sequenced as follows: twenty plants from each petri dish were pooled separately and DNA was extracted using the CTAB method (dx.doi.org/10.17504/protocols.io.quidwue). Following the mobilome-seq method described in (Lanciano et al., 2017), for all samples, we digested linear DNA from 2 µg of total DNA for 17 hours at 37<sup>o</sup>C using 10 U of PlasmidSafe (<em>LubioScience cat# E3101K</em>), followed by enzyme denaturation (30 mins at 70<sup>o</sup>C). Digested DNA was precipitated with isopropanol supplemented with 1 µg of GlycoBlue coprecipitant (<em>Fisher Scientific cat# 10391565</em>). Circular DNA was then amplified through rolling circle amplification (RCA) with the Illustra TempliPhi kit (<em>GE Healthcare cat# 25-6400-10</em>), following the manufacturer recommendation and leaving the reaction for 16h at 30<sup>o</sup>C. DNA was once again precipitated with isopropanol and sent for Illumina paired end 150 bp sequencing at BGI, Hong Kong. Samples identification: eccDNA_A.thaliana_ctrl: control reads eccDNA_A.thaliana_HS: heat stressed plants reads eccDNA_A.thaliana_AZ_HS: reads of alpha-amanitin, zebularine and heat-stressed plants "R1" indicates forward and "R2" reverse reads.
