RNA-seq of total RNA from human adipose tissue stem cells induced to adipogenesis and osteogenesis for 24 hours
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Homo sapiens
SUBMITTER: Patrícia Shigunov
PROVIDER: E-MTAB-6298 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Here we used activating (purmorphamine) and blocking (cyclopamine) drugs characterized of the Hedgehog pathway in adipose tissue-derived stem cells and identified mRNAs associated polysomes or free fraction in each condition.
2018-08-24 | E-MTAB-6254 | biostudies-arrayexpress
Project description:Differentiation of mesenchymal stem cells into adipocytes was studied. Control (undifferentiated) stem cells were compared to induced (3 days of induction) cells. In addition, two RNA fractions are studied: RNA associated to polysomes and total RNA.
2013-07-10 | E-MTAB-1366 | biostudies-arrayexpress
Project description:Purpose: we want to see gene expression changes during in vitro expansion of VM-derived NSCs (VM-NSCs) with cell passges in the absence or presence of Lin28a overexpression. changes upon Lin28 overexpression in P1 and P3 stages of Neural stem cells. RNA-seq, sRNA-seq, and Polysome-seq with/without Lin28 overexpression in P1 and P3 stages of Neural stem cells.
2016-08-11 | E-GEOD-77851 | biostudies-arrayexpress
Project description:Techniques for systematically monitoring protein translation have lagged far behind methods for measuring mRNA levels. Here we present a ribosome profiling strategy, based on deep sequencing of ribosome protected mRNA fragments, that enables genome-wide investigation of translation with sub-codon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control both for determining absolute protein abundance and for responding to environmental stress. We also observed distinct phases during translation involving a large decrease in ribosome density going from early to late peptide elongation as well as wide-spread, regulated initiation at non-AUG codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible. Examine replicates of ribosome footprints and mRNA abundance in biological replicates of log-phase growth and acute amino acid starvation
2009-02-12 | E-GEOD-13750 | biostudies-arrayexpress
Project description:Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the former has been studied extensively, to what extent translation occurs on monosomes and its importance for overall translational output remains controversial. Here, we used ribosome profiling to examine the translational status of 80S monosomes in Saccharomyces cerevisiae. We found that the vast majority of 80S monosomes are elongating, not initiating. Further, most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on nonsense-mediated decay (NMD) targets, upstream open reading frames (uORFs), canonical ORFs shorter than ~590 nucleotides and ORFs for which the total time required to complete elongation is substantially shorter than that required for initiation. Importantly, mRNAs encoding low-abundance regulatory proteins tend to be enriched in the monosome fraction. Our data highlight the importance of monosomes for the translation of highly regulated mRNAs. We examined the translational status of single 80S ribosomes using ribosome profiling, and compared these monosome footprints to both polysome ribosome footprints and general ribosome profiling. RNASeq libraries were also prepared from the overall sample input.
2016-02-11 | E-GEOD-76117 | biostudies-arrayexpress
Project description:The goal of this study was to compare the radiation-induced gene translation profiles generated from human tumor cell lines that are treated with radiation. Keywords: stimulus or stress design A panel of cell lines included 5 gliomas, 4 pancreatic carcinomas, 3 breast carcinomas and 2 non-small cell lung carcinomas. In addition, radiation-induced gene translation profiles were generated for 4 normal human cell lines: a skin fibroblast (BJ), 2 lung fibroblasts (MRC5, MRC9) and mammary epithelial (MEC). Specifically, cell lines were exposed to 2 Gy or sham irradiated, polysome-bound RNA was isolated 6h later and subjected to microarray analyses. Each cell line was evaluated in biological replicates.
2010-07-20 | E-GEOD-10547 | biostudies-arrayexpress
Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions. Examination of mRNA translation in S. cerevisiae upon glucose starvation.
2014-07-28 | E-GEOD-56622 | biostudies-arrayexpress
Project description:The gene expression of Trypanosoma brucei has been examined extensively in the blood of mammalian hosts and in forms found in the midgut of its arthropod vector, the tsetse fly. However, trypanosomes also undergo development within the mammalian bloodstream as they progress from morphologically M-bM-^@M-^Xslender formsM-bM-^@M-^Y to transmissible M-bM-^@M-^Xstumpy formsM-bM-^@M-^Y through morphological intermediates. This transition is temporally progressive within the first wave of parasitaemia such that gene expression can be monitored in relatively pure slender and stumpy populations as well as during the progression between these extremes. The development also represents the progression of cells from translationally active forms adapted for proliferation in the host to translationally quiescent forms, adapted for transmission. We have used metabolic labelling to quantitate translational activity in slender forms, stumpy forms and in forms undergoing early differentiation to procyclic forms in vitro. Thereafter we have examined the cohort of total mRNAs that are enriched in throughout development in the mammalian bloodstream (slender, intermediate and stumpy forms), irrespective of strain, revealing those that exhibit consistent developmental regulation rather than sample specific changes. Transcripts that cosediment with polysomes in stumpy forms and slender forms have also been identified to enrich transcripts that escape translational repression prior to transmission. Combined, the expression and polysomal association of transcripts as trypanosomes undergo development in the mammalian bloodstream haves been defined, providing a resource for trypanosome researchers. This facilitates the identification of those that undergo developmental regulation in the bloodstream and therefore those likely to have a role in the survival and capacity for transmission of stumpy forms. Examination of gene expression during life cycle stages.
2013-12-16 | E-GEOD-46388 | biostudies-arrayexpress
Project description:Ribosome profiling performed on interspecific hybrids of Sacharromyces cerevisiae and S. paradoxus in order to identify allele-specific expression indicative of cis-regulatory divergence at the level of mRNA abundance and protein translation. Two biological replicate libraries sequenced from ribosome protected fragments as well as poly-A-selected mRNA of hybrids in addition to one biological replicate library of poly-A selected mRNA from each parental strain.
2013-11-29 | E-GEOD-50049 | biostudies-arrayexpress
Project description:Effect of insulin on the cardiomyocyte global transcriptome and RNAs recruited to polysomes. <br>For comparison with endothelin-1
2010-07-04 | E-MEXP-2527 | biostudies-arrayexpress