Contributors:Rougeot, Julien, Chrispijn, Naomi D., Aben, Marco, Elurbe, Dei M., Andralojc, Karolina M., Murphy, Patrick J., Jansen, Pascal WTC, Vermeulen, Michiel, Cairns, Bradley R., Kamminga, Leonie M.
This dataset contains zebrafish (Danio rerio) raw RNA and ChIP sequencing data:
RNAseq_Wildtype_rep.fastq.gz: 2 biological replicates of single-end RNA-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates
RNAseq_Wildtype_rep[3-6].fastq.gz 4 biological replicates of paired-end RNA-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates
lane1_MPZezh2WT-24hpf-Ezh2__R.fastq.gz: 1 sample of paired-end Ezh2 ChIP-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates
lane1_MPZezh2WT-24hpf-Rnf2__R.fastq.gz: 1 sample of paired-end Rnf2 ChIP-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates
lane1_MPZezh2WT-24hpf-H3K27me3__R.fastq.gz: 1 sample of paired-end H3K27me3 ChIP-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates
*MPZezh2WT-24hpf-H3K4me3*: 2 biological replicates of paired-end H3K4me3 ChIP-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates
MPZezh2WT-24hpf-Ezh2-spikein-13277_R.fastq.gz: 1 sample of paired-end Ezh2 ChIP-seq data (with Drosophila H2Ay spike in) from 24hpf wild-type (TU/TL background) whole embryo lysates
MPZezh2WT-24hpf-H3K27A[cC]*: 2 biological replicates of paired-end H3K27ac ChIP-seq data from 24hpf wild-type (TU/TL background) whole embryo lysates
MPZezh2WT-24hpf-H3K27me3-spikein-13275_R.fastq.gz: 1 sample of paired-end H3K27me3 ChIP-seq data (with Drosophila H2Ay spike in) from 24hpf wild-type (TU/TL background) whole embryo lysates
Contributors:Conesa, Ana, Madrigal, Pedro, Tarazona, Sonia, Gomez-Cabrero, David, Cervera, Alejandra, McPherson, Andrew, Szcześniak, Michał Wojciech, Gaffney, Daniel J., Elo, Laura L., Zhang, Xuegong, Mortazavi, Ali
RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.
Parkinson disease (PD) is characterized by a loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc). The selective loss of this cell population makes PD a good candidate for cell-based therapies. Clinical trials using cells derived from human fetal ventral midbrain (hVM) have shown that dopamine release was restored to normal levels and in some PD patients produced substantial long-term clinical improvement. Although new sources of cells such as human embryonic stem cells (hESCs) and pluripotent stem cells (IPCs) are now been the focus of studies and new clinical trials, the hVM tissue represent the gold standard for cell based therapies and serve as important comparator for new cell sources. Therefore there is a need of an increased understanding and characterization of this tissue with new technologies such as organoid culture conditions and single cell sequencing. This study is designed to give a detailed characterization of human fetal VM tissue in standard culture conditions (2D) versus organoids (3D). We used immunocytochemistry to study the presence of ventral midbrain markers in 2D versus 3D condition together with single cell RNA sequencing to transcriptionally compare fetal VM tissue in standard or organoid cultures.
Our analysis confirmed that the 3D condition preserve the neuronal composition of the tissue more than standard culture where instead, over a long period of time, the majority of the cells are non-neuronal. This suggest that 3D culture represent a better condition to maintain and study dopaminergic neurons in culture.
Contributors:Kirov, Ilya, Gilyok, Marina, Knyazev, Andrey, Fesenko, Igor
Satellite DNA (satDNA) constitutes a substantial part of eukaryotic genomes. In the last decade, it has been shown that satDNA is not an inert part of the genome and its function extends beyond the nuclear membrane. However, the number of model plant species suitable for studying the novel horizons of satDNA functionality is low. Here, we explored the satellitome of the model "basal" plant, Physcomitrella patens (Hedwig, 1801) Bruch & Schimper, 1849 (moss), which has a number of advantages for deep functional and evolutionary research. Using a newly developed pyTanFinder pipeline (https://github.com/Kirovez/pyTanFinder) coupled with fluorescence in situ hybridization (FISH), we identified five high copy number tandem repeats (TRs) occupying a long DNA array in the moss genome. The nuclear organization study revealed that two TRs had distinct locations in the moss genome, concentrating in the heterochromatin and knob-rDNA like chromatin bodies. Further genomic, epigenetic and transcriptomic analysis showed that one TR, named PpNATR76, was located in the intergenic spacer (IGS) region and transcribed into long non-coding RNAs (lncRNAs). Several specific features of PpNATR76 lncRNAs make them very similar with the recently discovered human lncRNAs, raising a number of questions for future studies. This work provides new resources for functional studies of satellitome in plants using the model organism P. patens, and describes a list of tandem repeats for further analysis.