Additional file 1: of Australian black field crickets show changes in neural gene expression associated with socially-induced morphological, life-history, and behavioral plasticity

Figure S1. Expression patterns (log2-transformed, median centered) of the two clusters showing significant differences in gene expression between early (Day 3) and late (Day 13). The blue line indicates the mean-centered expression patterns of each cluster. The grey lines indicate individual expression patterns of each gene. Figure S2. Flowchart showing the workflow for the transcriptome assembly, evaluation and annotation. Table S1. The percentage of reads mapped to the three transcriptomes assembled by different assemblers. Table S2. Statistics of the assembled transcriptomes by different assemblers and redundancy removal steps. (DOCX 1765 kb

Additional file 3: of Australian black field crickets show changes in neural gene expression associated with socially-induced morphological, life-history, and behavioral plasticity

Supplementary Excel file (XLSX 29 kb

Additional file 3: Figure S1. of Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

Venn diagrams of the DEGs comparing 3 biological replicates from the SE data with 2 biological replicates from the PE data. (PPTX 237 kb

Additional file 2: Table S1. of Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols

Numbers of DEGs found using 2 biological replicates with PE and 3 biological replicates with SE. (XLSX 42 kb

OTUreporter: a modular automated pipeline for the analysis and report of amplicon data

While 16S rRNA gene amplicon sequencing is not considered a state-of-the-art technique any more, it is now considered a well-matured technique for the routine screening of samples of microbiological interest. The maturity of the technique with the lower costs, have provided an increased demand even in areas foreign to typical research.<br> <br> OTUreporter was developed aiming to bridge the gap between a sequencing service provider without dedicated bioinformatics personnel, and a non-expert customer. OTUreporter was also designed keeping in mind customers with limited computing resources for the initial stages of the amplicon data analysis.<br> <br> Unlike many automated 16S rRNA gene amplicon tools such those made available by sequencing companies (e.g. Illumina's "16S Metagenomics" tool), OTUreporter is not a "black box" and uses software that it is actually used in research context for this matters.<br> <br> OTUreporter accesses BaseSpace directly to gather amplicon data and sequencing run details, avoiding any need for the manual download. The main program used in the background is mothur. OTUreporter uses a slightly modified version of the MiSeqSOP protocol for processing the amplicon data.<br> <br> The final output of OTUreporter is a report. The report summarises the details, not only of the analysis, but also of the sequencing jobs themselves. The report, based on a RMarkdown template, creates two different outputs of the same report: a slimmer printer-friendly pdf document, and an extended html output with interactive content.<br> <br><div> OTUreporter is currently in beta testing at the Ramaciotti Centre for Genomics.</div><div><br></div><div>If you use OTUreporter or reuse any of its contents, please cite the repository at Bitbucket (https://bitbucket.org/xvazquezc/otureporter) or this poster as: <br></div><div>Vázquez-Campos, X., Chilton, A., Koval, J., Tree, J. J., & Wilkins, M. R. OTUreporter: a modular automated pipeline for the analysis and report of amplicon data. Sydney Bioinformatics Research Symposium 2018. 15 Jun 2018. Sydney, NSW, Australia. DOI: <a rel="noreferrer noopener" target="_blank">10.6084/m9.figshare.6521171.</a><br><br></div

Additional file 5: Table S5. of RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome

Searches for GTF2IRD1 interaction partners in the BioGRID and MetaCore databases. (XLSX 51 kb

Additional file 2: Table S2. of RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome

Gene ontology analysis performed with the BiNGO plug-in to Cytoscape. The lists of up-regulated and down-regulated genes were analysed for enrichment of gene ontology terms using BiNGO. The results are presented in this file. The results of gene ontology analysis for the DE transcription factors are also in this file. (XLSX 154 kb

Additional file 4: Table S4. (Tables S1–S7) of RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome

Categorisation of Subsets of differentially expressed genes. This file includes tables of genes found to be differentially expressed which are involved in growth factor signalling (Table S1), cytokine signalling (Table S2), Wnt signalling (Table S3), Calcium signalling (Table S4), Cell cycle (Table S5), Hedgehog signalling (Table S6) and G protein-coupled signalling (Table S7). (XLSX 89 kb

Additional file 6: Table S6. of RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome

Primers used in RTqPCR validation. (XLSX 10 kb

A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B

<div><p>The replacement of histone H2A with its variant forms is critical for regulating all aspects of genome organisation and function. The histone variant H2A.B appeared late in evolution and is most highly expressed in the testis followed by the brain in mammals. This raises the question of what new function(s) H2A.B might impart to chromatin in these important tissues. We have immunoprecipitated the mouse orthologue of H2A.B, H2A.B.3 (H2A.Lap1), from testis chromatin and found this variant to be associated with RNA processing factors and RNA Polymerase (Pol) II. Most interestingly, many of these interactions with H2A.B.3 (Sf3b155, Spt6, DDX39A and RNA Pol II) were inhibited by the presence of endogenous RNA. This histone variant can bind to RNA directly <i>in vitro</i> and <i>in vivo</i>, and associates with mRNA at intron—exon boundaries. This suggests that the ability of H2A.B to bind to RNA negatively regulates its capacity to bind to these factors (Sf3b155, Spt6, DDX39A and RNA Pol II). Unexpectedly, H2A.B.3 forms highly decompacted nuclear subdomains of active chromatin that co-localizes with splicing speckles in male germ cells. H2A.B.3 ChIP-Seq experiments revealed a unique chromatin organization at active genes being not only enriched at the transcription start site (TSS), but also at the beginning of the gene body (but being excluded from the +1 nucleosome) compared to the end of the gene. We also uncover a general histone variant replacement process whereby H2A.B.3 replaces H2A.Z at intron-exon boundaries in the testis and the brain, which positively correlates with expression and exon inclusion. Taken together, we propose that a special mechanism of splicing may occur in the testis and brain whereby H2A.B.3 recruits RNA processing factors from splicing speckles to active genes following its replacement of H2A.Z.</p></div