DataSim-Evolution2011.tar

Simulation data file. It contains simulated species trees and gene trees, as well as the inferred gene trees from simulated DNA sequences. It also contains a README file

Additional file 1 of Detecting circular RNA from high-throughput sequence data with de Bruijn graph

Additional file 1 Supplemental materials for “Detecting Circular RNA from High-throughput Sequence Data with de Bruijn Graph”

Additional file 1 of Detecting genomic deletions from high-throughput sequence data with unsupervised learning

Additional file 1. Supplemental materials for “Calling genomic deletions from sequence data using unsupervised learning”. It contains the additional results presented in this paper. “A F1 score of NA12878 in each chromosome” contains the results of F1 score for each chromosome in NA12878 respectively. “B Command lines used for genomic deletions detection” is about the command lines used by each tool for deletion detection

Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice

<div><p>Nucleosome positioning dictates the DNA accessibility for regulatory proteins, and thus is critical for gene expression and regulation. It has been well documented that only a subset of nucleosomes are reproducibly positioned in eukaryotic genomes. The most prominent example of phased nucleosomes is the context of genes, where phased nucleosomes flank the transcriptional starts sites (TSSs). It is unclear, however, what factors determine nucleosome positioning in regions that are not close to genes. We mapped both nucleosome positioning and DNase I hypersensitive site (DHS) datasets across the rice genome. We discovered that DHSs located in a variety of contexts, both genic and intergenic, were flanked by strongly phased nucleosome arrays. Phased nucleosomes were also found to flank DHSs in the human genome. Our results suggest the barrier model may represent a general feature of nucleosome organization in eukaryote genomes. Specifically, regions bound with regulatory proteins, including intergenic regions, can serve as barriers that organize phased nucleosome arrays on both sides. Our results also suggest that rice DHSs often span a single, phased nucleosome, similar to the H2A.Z-containing nucleosomes observed in DHSs in the human genome.</p></div

Assembly quality comparison of REPdenovo and RepARK.

N: the number of assembled contigs. Nh: the number of complete Repbase hits from the N repeats (with 85% coverage cutoff). : average coverage of hits. Cm: maximum coverage of hits by single assembled repeats. N50: N50 of assembled repeats.</p

Sequence reads information from four human individuals from the 1000 Genomes Project.

# of reads: in millions. Coverage: average sequence depth per base.</p

Numbers of repeats that hit Repbase (with matching cutoff 0.0) and masked by RepeatMasker (with matching cutoff 0.0).

<p>We classify the repeats based on whether they are mappable to the human reference and whether they have matches in Repbase. Masked: RepeatMasker can classify the repeat. Unmasked: RepeatMasker cannot classify the repeat.</p

The number of repeats in Repbase that match (over the minimum threshold <i>t</i>_<i>L</i>) one <i>de novo</i> repeat.

<p>The numbers outside and side the parentheses are REPdenovo and RepARK results, respectively. <i>t</i>_<i>L</i>: matching cutoff.</p

Phased nucleosome arrays flanked TSSs of rice genes.

<p>(A) Nucleosome positioning profile associated with active genes. Phased nucleosome arrays are detectable after the TSSs. (B) Nucleosome positioning profile associated with non-expressed genes. Phased nucleosome arrays are detected on either side of the TSSs. (C) Distribution of DHS length for five different DHS categories. Note: the length of DHSs associated with proximal promoters (black line) are more variable than the lengths of other DHSs. (D) Heatmap of nucleosome positioning associated with active genes. Left panel: All expressed genes were sorted by the length of DHSs located in proximal promoters. The 5′ ends of the MNase-seq reads were mapped within 1 kb upstream and 1 kb downstream of the TSS of each gene to show the boundaries of nucleosomes core and linker. The red line on the left heatmap indicates the boundaries of DHSs. With the same order of the genes as in the left panel, the 5′ ends of DNase-seq reads (middle panel) and the fragments per kilobase of exon per million fragments mapped (FPKM) value log10 transformation (right panel) were mapped to show the DNase I sensitivity and the expression level of each gene, respectively.</p

Association IPA1-binding sites with phased nucleosomes.

<p>An example of phased nucleosome arrays that flank an intergenic IPA1-binding site on rice chromosome 8. This binding site is overlapped with a DHS (red arrow). The distribution of MNase-seq data (dyad density calculated from paired-end reads by NucleR) and DNase-seq data (density calculated by F-seq) were used to present the nucleosome and DHS positions. Phased nucleosomes and DHS regions were also schematically marked.</p