Generation of transcriptional novelty by transposable element insertions in Arabidopsis, Genome Sequencing and eccDNA Data

Raw Illumina sequencing data from the Manuscript entitled "Generation of transcriptional novelty by transposable element insertions in Arabidopsis" A. Illumina genome sequencing reads of Arabidopsis control and hcLines that contain novel transposable element insertions. To identify the genomic position of the new ONSEN 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. B. Illumina eccDNA sequencing of Arabidopsis control and hcLines following stress treatments 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 37oC using 10 U of PlasmidSafe (LubioScience cat# E3101K), followed by enzyme denaturation (30 mins at 70oC). Digested DNA was precipitated with isopropanol supplemented with 1 µg of GlycoBlue coprecipitant (Fisher Scientific cat# 10391565). Circular DNA was then amplified through rolling circle amplification (RCA) with the Illustra TempliPhi kit (GE Healthcare cat# 25-6400-10), following the manufacturer recommendation and leaving the reaction for 16h at 30oC. 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