Project description:P. nigra × P. maximowiczii plants were grown in the field, each in monoculture and in stands mixed with Robinia pseudoacacia, at two locations differing in soil nutrient levels. After 3 years of growing under ambient weather conditions, leaf samples were harvested and analyzed by RNA-seq.
Project description:P. nigra × P. maximowiczii plants were grown in the field, each in monoculture and in stands mixed with Robinia pseudoacacia, at two locations differing in soil nutrient levels. After 4 years of growing under ambient weather conditions, leaf samples were harvested and analyzed by RNA-seq.
Project description:Detect the global transcriptional changes occuring during spreading and maintenance of systemic post transcriptional silencing . Test the hypothesis that activation of systemic PTGS induces parallel antiviral defense pathways. Gene expression was analysed by MACE method (Massive Analysis of cDNA Ends) on total RNA extracted from leaf tissues of WT plants (WT), and GFP6.4 presenting no-silencing (NS sample), ongoing spreading of silencing (OS) and maintenance of silencing (SS). Plants were grown in parallel, and silencing state was monitored under UV. After 3 weeks of growth, total RNAs were extracted using the Trizol method from leaf tissues of 2-3 leaf stage plants. A total of 4 plants were sampled per variable (WT/NS/OS/SS). RNA from 4 plants were pooled and sequenced.
Project description:Subtelomeric chromatin is subject to evolutionarily conserved complex epigenetic regulation and is implicated in numerous aspects of cellular function including formation of heterochromatin, regulation of different stress response pathways, and control of lifespan. Subtelomeric DNA is characterized by the presence of specific repeated segments that serve to propagate silencing activities or to protect chromosomal regions from spreading epigenetic control. Using condition-specific genome wide chromatin immunoprecipitation and expression data, we show that several yeast transcription factors regulate subtelomeric silencing in response to various environmental stimuli through conditional association with proto-silencing regions called X elements. In this context, some factors control the propagation of silencing toward centromeres in response to stimuli affecting stress responses and metabolism, whereas others appear to influence boundaries of silencing, regulating telomere-proximal genes in Y’ elements. The factors implicated here have previously been shown to control adjacent genes at intrachromosomal positions, suggesting dual functionality of the factors and a possible mechanism of coordinating intrachromosomal gene expression with subtelomeric silencing. These data suggest a fundamental mechanism to coordinate telomere biology related to aging and adaptation with cellular environment and the activities of other cellular processes. These are Chip-CHIP data for myc tagged Oaf1p transcription factor from S. cerevisiae grown in the presence or absence of the fatty acid oleate. ChIP-CHIP analysis was performed to determine the genomic distribution of Oaf1p transcription factor in the BY4742 yeast strain after growth in 0.1% glucose, or in the presence of the fatty acid oleate. Three biological replicates for each growth condition (in the presence of low glucose or 5 h after a shift to medium containing oleate as a carbon source). ChIP samples were amplified by PCR, labelled and hybridized to 50-mer tiling arrays covering both strands of the entire yeast genome at a 64 bp resolution.
Project description:Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is an anaplastic lymphoma kinase-negative (ALKneg) T-cell lymphoma. Here, we provide RNA-seq data of four BIA-ALCL and four ALCL cell lines:TLBR-1, TLBR-2, TLBR-3, TLBR-4 and DEL (two replicates), KARPAS-299, KI-JK, SUP-M2 (two replicates), respectively.
Project description:Early B-cell development is primarily regulated at the transcriptional level and comprises the consecutive differentiation stages B-cell progenitor, pro-B-cell and pre-B-cell. These entities provide the cells of origin in B-cell precursor acute lymphoid leukemia (BCP-ALL) which show deregulation of developmental transcription factors (TFs), representing major oncogenic drivers. Analysis of TF activities in these developmental entities helps understanding both their normal and aberrant expression and regulatory connections. Here, we focused on NKL-subclass homeodomain TF NKX6-3 which is active in normal B-cell progenitors and TCF3::PBX1-positive BCP-ALL cases. Performing siRNA-mediated knockdown and forced expression experiments in BCP-ALL model cell lines, we established a gene regulatory network for NKX6-3 together with NKL-TFs HLX, MSX1 and HHEX, TALE-class homeodomain TFs MEIS1 and IRX1, ETS-TFs ERG, ETS2 and SPIB, and additionally with PAX5, EBF1 and IRF4. NKX6-3 and TCF3::PBX1 were found to be mutual activators, underlying their co-expression. Furthermore, comparative expression profiling analysis of BCP-ALL patients revealed TGFb-pathway inhibitor CD109 as downregulated target gene of NKX6-3. TGFb in turn enhanced NKX6-3 expression, indicating mutual activation. Finally, RNA-seq analysis of BCP-ALL cell line RCH-ACV after NKX6-3 knockdown revealed MPP7 as upregulated target gene of both, NKX6-3 and TCF3::PBX1. Elevated MPP7 expression indicated an oncogenic role of the HIPPO-pathway in TCF3::PBX1 positive BCP-ALL. Collectively, our data add novel players and regulatory connections to normal and aberrant TF-networks in B-cell progenitors which may serve as diagnostic markers or therapeutic targets.
Project description:Despite ethical concerns and scientific drawbacks, fetal bovine serum (FBS) remains a common supplement of culture media for continuous cancer cell lines. FBS alternatives like human platelet lysate (hPL) as well as animal-component free, chemically defined media (CDM) are commercially available for many years. Nevertheless, the acceptance of such alternative media is limited because data verifying the stability of the phenotype and function of a cell line in the alternative media are often lacking. Here, we have adapted four widely used human cancer cell lines (HELA, HL-60, JIMT-1, K-562) to hPL supplemented media and different CDM. To evaluate the suitability of the FBS-free replacements in comparison to the FBS media, we systematically analyzed the different cultures in respect to recovery after cryopreservation, STR-profiles, proliferation, morphology and their transcriptomes. Neither alterations in STR-profiles nor difficulties after cryopreservation were detected. With the exception of K-562, FBS-free cultures showed a reduced proliferation rate and, in some conditions, slight morphological alterations in comparison to FBS cultures. Transcriptome-wide GSEA indicated that culture media affected expression of genes involved in cholesterol homeostasis in all cell lines, and genes involved in epithelial-mesenchymal transition in HELA and JIMT-1. However, their overall phenotypes remained stable. Hematopoietic differentiation markers were among the differentially expressed genes of HL-60 and K-562 cultures, but their main phenotypes remained very similar which was further confirmed by successful induction of differentiation of HL-60 in FBS-free media. In summary, our multiparametric approach delivers validated data supporting the transition to FBS-free media for the analyzed cancer models.
Project description:Continuous cell lines are important and commonly used in vitro models in breast cancer (BC) research. Selection of the appropriate model cell line is crucial and requires consideration of their molecular characteristics. To characterize BC cell line models in depth, we profiled a panel of 29 authenticated and publicly available BC cell lines by mRNA-sequencing, mutation analysis, and immunoblotting. Gene expression profiles separated BC cell lines in two major clusters that represent basal-like (mainly triple-negative BC) and luminal BC subtypes, respectively. HER2-positive cell lines were located within the luminal cluster. Mutation calling highlighted the frequent aberration of TP53 and BRCA2 in BC cell lines, which, therefore, share relevant characteristics with primary BC. Furthermore, we showed that the data can be used to find novel, potential oncogenic fusion transcripts, e.g., FGFR2::CRYBG1 and RTN4IP1::CRYBG1 in cell line MFM-223, and to elucidate the regulatory circuit of IRX genes and KLF15 as novel candidate tumor suppressor genes in BC. Our data indicated that KLF15 was activated by IRX1 and inhibited by IRX3. Moreover, KLF15 inhibited IRX1 in cell line HCC-1599. Each BC cell line carries unique molecular features. Therefore, the molecular characteristics of BC cell lines described here might serve as a valuable resource to improve the selection of appropriate models for BC research. Raw fastq files are also published at BioStudies: S-BSST1200.
Project description:Roots were collected from young trees outplanted in three regions in Germany (Schorfheide, Swabian Alb, Hainich) and used for RNA extraction. In each region four plots were sampled. Two plants used from each plot. The RNA of the plants per plot was pooled. Four technical replicates were prepared.