Project description:The aim of this experiment was to develop new methods to extract pure fractions of nuclear and cytoplasmic RNA. We compared the results of nuclear and cytoplasmic RNA-sequencing to results of the total and polyA+ RNA-sequencing. Cytoplasmic, nuclear, total and polyA+ RNA was extracted from two human brain samples and sequenced on the SOLiD system. We analyzed the data to look for differences in levels of nascent transcription and mature mRNAs between the different samples.
Project description:The response to DNA damage intersects with many other physiological processes in the cells, including initiation of DNA repair, regulation of transcription and translation, chromatin remodeling, and the cell cycle regulation to contend with the challenge. Transcription shutdown is not simply a consequence of the physical arrest of RNA polymerase II by DNA lesions, but also could be elicited by signaling in trans. While to date many of the specific molecular events are not fully elucidated. What is the signal that operates in trans to slow transcriptional elongation globally? Which factors are required for transcription restart after DNA repair? How is TC-NER controlled by the multifaceted transcriptional response? In this study, we sought to map the transcription restart and isolate the set of lncRNAs that are likely to function at the chromatin interface by using biochemical fractionation of the cellular compartment coupled to RNA-seq.
Project description:We isolated whole embryo, nuclear, and cytoplasmic lysates from Drosophila embryos during early and late embryogenesis In Drosophila melanogaster, cell-type specification during early nervous system development requires precise regulation of gene expression in time and space. To investigate the gene regulation patterns in early neuronal development, we developed a method 'DIV-SortSeq' to enrich for specific neuroglial cell types for RNA sequencing: from early columnar subdivision and specification, through neuroglial differentiation. DIV-SortSeq recapitulates many of the known protein-coding transcriptome dynamics, as well as novel transcriptional regulatory patterns. We also performed nuclear-cytoplasmic fractionation of whole embryos - Fractionation-Seq - to assess temporal changes in subcellular localization of transcripts during embryogenesis. We present these data as a resource to permit further in-depth investigation into the functional roles of the coding and noncoding transcriptome during early Drosophila neurogenesis.
Project description:The membrane fraction and the cytosolic fraction of HES2 cells were collected and subjected to microarray. The experiment was performed in triplicate Keywords: membrane-polysome fractionation of RNA
