Small RNA Next Generation Sequencing of human primary macrophages treated with staurosporine
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE47608 | GEO | 2015/09/16
SECONDARY ACCESSION(S): PRJNA206510
REPOSITORIES: GEO
Similar Datasets
Project description:Human primary macrophages were treated with 1 µM staurosporine (STS) and profiled for small RNAs. Human primary macrophages were treated with 1 µM staurosporine (STS) for 0, 4 and 6h.
2015-09-16 | E-GEOD-47608 | biostudies-arrayexpress
Project description:Staurosporine induces programmed cell death in a series of organisms. Here, we analyse gene expression of the filamentous fungus Neurospora crassa following exposure to staurosporine for different time periods.
2011-09-30 | GSE32451 | GEO
Project description:Macrophages are important for mounting inflammatory responses to tissue damage or infection by invading pathogens, and therefore modulation of their cellular functions is essential for the success of the immune system as well as for maintaining tissue homeostasis. Small non-coding RNAs are important regulatory elements of gene expression and microRNAs are the most widely known to be fundamental for the proper development of cells of the immune system. Macrophages can exhibit different phenotypes, depending on the cytokine environment they encounter in the affected tissues. We have analyzed the microRNA expression profiles during maturation of human primary monocytes into macrophages and polarization by pro- or anti-inflammatory cytokines. Here we describe the analysis of next-generation sequencing data deposited in EMBL-EBI ArrayExpress under accession number E-MTAB-1969 and associated with the study published by Cobos Jiménez and collaborators in Physiological Genomics in 2014 (1). The data presented here contributes to our understanding of microRNA expression profiles in human monocytes and macrophages and will also serve as a resource for novel microRNAs and other small RNA species expressed in these cells.
| S-EPMC4535945 | biostudies-literature
Project description:Staurosporine induces programmed cell death in a series of organisms. Here, we analyse gene expression of the filamentous fungus Neurospora crassa following exposure to staurosporine for different time periods. Cells incubated for 15, 30, 60 and 120 min in the presence (S) or absence (C) of staurosporine were compared; Cy3 and Cy5 dye swap
2011-09-29 | E-GEOD-32451 | biostudies-arrayexpress
Project description:Analysis of small RNAs that are deregulated in apoptotic macrophages
2015-10-15 | GSE63799 | GEO
Project description:Purpose: Compare the transcriptional profile of staurosporine-treated cells in Neurospora crassa wild type and Δczt-1 (ΔNCU09974) cells Methods: Conidial suspensions were obtained and 1 x 106 cells/ml incubated in minimal medium for 6 hours (26ºC, 140 rpm, constant light) followed by the addition of staurosporine (or DMSO) and growth for 1 more hour. Cells were harvested using 0.45 μm filters and immediately frozen in liquid nitrogen. Total RNA was isolated by the Trizol-Phenol-Chloroform method. After digestion of 25 μg RNA with TURBO DNAse (Life Technologies), mRNA was purified using Dynabeads oligo(dT) magnetic beads (Life Technologies). The mRNA was chemically fragmented using the Ambion RNA fragmentation kit (Life Technologies). First and second strand cDNA synthesis was achieved using appropriate kits (Life Technologies). The illumina TruSeq kit was employed to generate the cDNA libraries with indexing adapters essentially following the manufacturer’s protocol. After purification of the libraries with AMPure XP beads (Roche), the quality of the libraries was analysed in a Agilent 2100 Bioanalyzer. The cDNA libraries were sequenced in a illumina HiSeq2000 and single reads of 50 bp were obtained. Sequencing data was handled essentially with Tophat, Cufflinks and Cuffdiff. Expression levels are presented as Fragments/Reads Per Kilobase of transcript per Million mapped reads (FPKM/RPKM). Results: Transcriptional profiling of staurosporine-treated cells wild type by RNA-sequencing showed that genes encoding the machinery for protein synthesis are enriched among the genes repressed by the drug. Functional category enrichment analyses also show that genes encoding components of the mitochondrial respiratory chain are downregulated by staurosporine, whereas genes involved in endoplasmic reticulum activities are upregulated. In contrast, a staurosporine-treated czt-1 deletion strain is unable to repress the genes for the respiratory chain and to induce the genes related with the endoplasmic reticulum, indicating a role for CZT-1 on the regulation of activity of these organelles. Conclusions: This transcriptional profiling study is framed in a comprehensive study on the role of the novel transcription factor CZT-1 (NCU09974) in Neurospora crassa.
2014-07-01 | GSE52153 | GEO
Project description:CD4+ T cells can differentiate into several subsets of effector T helper cells depending on the surrounding cytokine milieu. Th17 cells can be generated from naïve CD4+ T cells in vitro by activating them in the presence of the polarizing cytokines IL-1?, IL-6, IL-23, and TGF?. Th17 cells orchestrate immunity against extracellular bacteria and fungi, but their aberrant activity has also been associated with several autoimmune and inflammatory diseases. Th17 cells are identified by the chemokine receptor CCR6 and defined by their master transcription factor, ROR?t, and characteristic effector cytokine, IL-17A. Optimized culture conditions for Th17 cell differentiation facilitate mechanistic studies of human T cell biology in a controlled environment. They also provide a setting for studying the importance of specific genes and gene expression programs through RNA interference or the introduction of microRNA (miRNA) mimics or inhibitors. This protocol provides an easy to use, reproducible, and highly efficient method for transient transfection of differentiating primary human Th17 cells with small RNAs using a next generation electroporation device.
| S-EPMC5564694 | biostudies-literature
Project description:Purpose: Compare the transcriptional profile of staurosporine-treated cells in Neurospora crassa wild type and M-NM-^Tczt-1 (M-NM-^TNCU09974) cells Methods: Conidial suspensions were obtained and 1 x 106 cells/ml incubated in minimal medium for 6 hours (26M-BM-:C, 140 rpm, constant light) followed by the addition of staurosporine (or DMSO) and growth for 1 more hour. Cells were harvested using 0.45 M-NM-<m filters and immediately frozen in liquid nitrogen. Total RNA was isolated by the Trizol-Phenol-Chloroform method. After digestion of 25 M-NM-<g RNA with TURBO DNAse (Life Technologies), mRNA was purified using Dynabeads oligo(dT) magnetic beads (Life Technologies). The mRNA was chemically fragmented using the Ambion RNA fragmentation kit (Life Technologies). First and second strand cDNA synthesis was achieved using appropriate kits (Life Technologies). The illumina TruSeq kit was employed to generate the cDNA libraries with indexing adapters essentially following the manufacturerM-bM-^@M-^Ys protocol. After purification of the libraries with AMPure XP beads (Roche), the quality of the libraries was analysed in a Agilent 2100 Bioanalyzer. The cDNA libraries were sequenced in a illumina HiSeq2000 and single reads of 50 bp were obtained. Sequencing data was handled essentially with Tophat, Cufflinks and Cuffdiff. Expression levels are presented as Fragments/Reads Per Kilobase of transcript per Million mapped reads (FPKM/RPKM). Results: Transcriptional profiling of staurosporine-treated cells wild type by RNA-sequencing showed that genes encoding the machinery for protein synthesis are enriched among the genes repressed by the drug. Functional category enrichment analyses also show that genes encoding components of the mitochondrial respiratory chain are downregulated by staurosporine, whereas genes involved in endoplasmic reticulum activities are upregulated. In contrast, a staurosporine-treated czt-1 deletion strain is unable to repress the genes for the respiratory chain and to induce the genes related with the endoplasmic reticulum, indicating a role for CZT-1 on the regulation of activity of these organelles. Conclusions: This transcriptional profiling study is framed in a comprehensive study on the role of the novel transcription factor CZT-1 (NCU09974) in Neurospora crassa. Transcriptional profile of wild type and M-NM-^Tczt-1 cells staurosporine-treated cells in Neurospora crassa was compared using illumina HiSeq2000 and single reads of 50 bp.
2014-07-01 | E-GEOD-52153 | biostudies-arrayexpress
Project description:In this study, we reporte the altered miRNAs expression in the human breast cancer cell line (MCF7) derived mammosphere in response to withaferin A IC50 concentrations (2 µM)..
2024-07-29 | GSE181099 | GEO
Project description:Array data from HeLa cells that remained Uninfected or were infected with wildtype S. flexneri serotype 2a strain 2457T. These groupings are further divided such that Uninfected or Infected cells remained untreated or were treated with the apopotosis inducer staurosporine (STS). The design of the experiment was a time course and samples were harvested at the indicated time points (hr). All hybridizations were conducted against a common reference sample. time_series_design
2010-06-12 | E-GEOD-22287 | biostudies-arrayexpress