Number of identical clusters as a function of minimum match number and multiplier

<p><b>Copyright information:</b></p><p>Taken from "Masking repeats while clustering ESTs"</p><p>Nucleic Acids Research 2005;33(7):2176-2180.</p><p>Published online 14 Apr 2005</p><p>PMCID:PMC1079970.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

Number of identical clusters as a function of the minimum gap size parameter

<p><b>Copyright information:</b></p><p>Taken from "Masking repeats while clustering ESTs"</p><p>Nucleic Acids Research 2005;33(7):2176-2180.</p><p>Published online 14 Apr 2005</p><p>PMCID:PMC1079970.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

List of chromosomes and crossover positions for the wt population

This is a tab-delimited text files with the format

Number of identical clusters as a function of the minimum length threshold

<p><b>Copyright information:</b></p><p>Taken from "Masking repeats while clustering ESTs"</p><p>Nucleic Acids Research 2005;33(7):2176-2180.</p><p>Published online 14 Apr 2005</p><p>PMCID:PMC1079970.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p

List of crossover positions for the recq4a mutant population

This is a tab-delimited text file with the format

<i>Arabidopsis thaliana</i> PacBio Iso-Seq output summary.

<p>cDNA was synthesised with Lexogen TeloPrime Full-Length amplification kit or the Clontech SMARTer PCR cDNA Synthesis Kit and then split into three size fractions (1–2, 2–3 and 3–6 kb), respectively. From left to right: number of transcript isoform clusters (HQ reads) assembled using the PacBio Iso-Seq pipeline; number of HQ reads aligning to the <i>A</i>. <i>thaliana</i> genome with a sequence identity > = 90%; percentage of full length HQ reads (FL) defined as the cumulative number of reads equal or larger in length than their respective target.</p

Improved resolution of transcription start and end sites in <i>T</i>. <i>aestivum</i>.

<p>Density plot of PacBio full-length cDNA read alignment ends within 10 kb around the target start and end coordinates are shown for each size fraction; (A) 1–2 kb size fraction; (B) 2–3 kb size fraction; (C) 3–6 kb size fraction. Vertical green dashed lines highlight target start and end sites.</p

Transcription start and end site enrichment using the TeloPrime Full-Length cDNA amplification kit (Lexogen).

<p>(A-C) Superimposed density plots of the PacBio Iso-Seq alignment coordinates against the 5’ and 3’ ends of their targets. TeloPrime cDNA libraries (red bars), SMARTer cDNA libraries (light blue bars), overlay of the two protocols (brown bars). (A) 1–2 kb size fraction; (B) 2–3 kb size fraction; (C) 3–6 kb size fraction. 10 kb around the annotated gene start and end coordinates are shown on the x-axis. Vertical green dashed lines highlight annotated target start and end sites.</p

Heat stress induces alternative splicing events.

<p><b>(A)</b> Examples of differentially expressed isoforms in response to heat stress in <i>A</i>. <i>lyrata</i>. AL3G42820 expresses a second isoform that lacks the middle exon in heat-treated samples (HS). Transcripts from wild-type (WT) and recovery (REC) samples contain all three exons. AL2G15640 retains an intron in response to heat stress (HS) while wild-type (WT) and recovery (REC) samples show partial intron splicing. <b>(B)</b> Number of differential splicing events, including alternative 5’ and 3’ splice sites, mutually exclusive exons, intron retention, and exon skipping events identified with MATs based on version-1 and version-2 annotations.</p

Examples of version-1 gene models split and merged in <i>A</i>. <i>lyrata</i> gene annotation version-2.

<p><b>(A)</b> Example of a gene model that was split into two gene models in version-2. Reverse transcription-PCR could not confirm the connection of both. <b>(B)</b> Example of version-1 gene models that were merged during the annotation update. Reverse transcription-PCR confirmed presence of a transcript bridging the two version-1 genes.</p