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Although accumulating evidence suggests that gene regulation is highly stochastic, genetic screens have successfully uncovered master developmental regulators, questioning the relationship between transcriptional noise and intrinsic robustness of development. To identify developmental modules that are more or less resilient to large-scale genetic perturbations, we used the Arabidopsis polymerase II-associated factor 1 complex (Paf1c) mutant vip3, which is impaired in several RNA polymerase II-dependent transcriptional processes. We found that the control of flower termination was not as robust as classically pictured. In angiosperms, the floral female organs, called carpels, display determinate growth: their development requires the arrest of stem cell maintenance. In vip3 mutant flowers, carpels displayed a highly variable morphology, with different degrees of indeterminacy defects up to wild-type size inflorescence emerging from carpels. This phenotype was associated with variable expression of two key regulators of flower termination and stem cell maintenance in flowers, WUSCHEL and AGAMOUS The phenotype was also dependent on growth conditions. Together, these results highlight the surprisingly plastic nature of stem cell maintenance in plants and its dependence on Paf1c.
Pubmed ID: 31540913
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Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsSoftware package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences.
View all literature mentionsSoftware ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
View all literature mentionsA commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis.
View all literature mentionsSoftware Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
View all literature mentionsSoftware tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.
View all literature mentionsCompany provides laboratories worldwide with analytical instruments and supplies, clinical and diagnostic testing services, consumables, applications and expertise in life sciences and applied chemical markets.
View all literature mentionsSoftware tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.
View all literature mentionsSoftware application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.
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