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Single cell RNA-seq data of human hESCs to evaluate Oscope - a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-Seq

ABSTRACT: Oscillatory gene expression is fundamental to mammalian development, but technologies to monitor expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applications to a number of data sets, include a single-cell RNA-seq data set of human embroyonic stem cells (hESCs), demonstrate advantages of the approach and also identify a potential artifact in the Fluidigm C1 platform.

ORGANISM(S): Homo sapiens

PROVIDER: GSE64016 | GEO | 2015/06/24

SECONDARY ACCESSION(S): PRJNA269761

REPOSITORIES: GEO

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Single cell RNA-seq data of human hESCs to evaluate Oscope - a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-Seq

Project description:Oscillatory gene expression is fundamental to mammalian development, but technologies to monitor expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applications to a number of data sets, include a single-cell RNA-seq data set of human embroyonic stem cells (hESCs), demonstrate advantages of the approach and also identify a potential artifact in the Fluidigm C1 platform. Total 213 H1 single cells and 247 H1-Fucci single cells were sequenced. The 213 H1 cells were used to evaluate Oscope in identifying oscillatory genes. The H1-Fucci cells were used to confirm the cell cycle gene cluster identified by Oscope in the H1 hESCs.

2015-06-24 | E-GEOD-64016 | biostudies-arrayexpress

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Project description:MDA 231 cells were cultured under hypoxia, normoxia, oscillatory hypoxia, and lactate and sequenced for RNA

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Oscillatory cAMP Signaling Rapidly Alters H3K4 Methylation

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Project description:This SuperSeries is composed of the following subset Series:; GSE7012: Identif. of oscillatory genes in somitogenesis from functional genomic analysis of C2C12 myoblast line; GSE7015: Identif. of oscillatory genes in somitogenesis from functional genomic analysis of a human mesenchymal stem cell model Experiment Overall Design: Refer to individual Series

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Extensive oscillatory gene expression during C. elegans larval development [Ribosome footprinting]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated.

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Identif. of oscillatory genes in somitogenesis from functional genomic analysis of C2C12 myoblast line

Project description:During somitogenesis, oscillatory expression of genes in the notch and wnt signaling pathways plays a key role in regulating segmentation. These oscillations in expression levels are elements of a species-specific developmental mechanism. To date, the periodicity and components of the human clock remain unstudied. Here we show that a human mesenchymal stem/stromal cell (MSC) model can be induced to display oscillatory gene expression. We observed that the known cycling gene HES1 oscillated with a 5 hour period, consistent with available data on the rate of somitogenesis in humans. We also observed cycling of Hes1 expression in mouse C2C12 myoblasts with a period of 2 hours, consistent with previous in vitro and embryonic studies. Furthermore, we used microarray and quantitative PCR (Q-PCR) analysis to identify additional genes that display oscillatory expression both in vitro and in mouse embryos. We confirmed oscillatory expression of the notch pathway gene Maml3 and the wnt pathway gene Nkd2 by whole mount in situ hybridization analysis and Q-PCR. Expression patterns of these genes were disrupted in Wnt3atm1Amc mutants but not in Dll3pu mutants. Our results demonstrate that human and mouse in vitro models can recapitulate oscillatory expression observed in embryo and that a number of genes in multiple developmental pathways display dynamic expression in vitro. Keywords: time series

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Transcription profiling of mouse C2C12 myoblast cell line to identify oscillatory genes in somitogenesis

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mRNA-seq time course of C. elegans sampled at and after release from dauer starvation at 25 degrees

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Rhythmic transcription drives mRNA level oscillations during C. elegans development [ChIP-Seq]

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