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Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE73354 | GEO | 2015/09/24

SECONDARY ACCESSION(S): PRJNA296781

REPOSITORIES: GEO

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Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization.

Project description:The use of time series profiling to identify groups of functionally related genes (synexpression groups) is a powerful approach for the discovery of gene function. Here we apply this strategy during Ras(V12) immortalization of Drosophila embryonic cells, a phenomenon not well characterized. Using high-resolution transcriptional time-series datasets, we generated a gene network based on temporal expression profile similarities. This analysis revealed that common immortalized cells are related to adult muscle precursors (AMPs), a stem cell-like population contributing to adult muscles and sharing properties with vertebrate satellite cells. Remarkably, the immortalized cells retained the capacity for myogenic differentiation when treated with the steroid hormone ecdysone. Further, we validated in vivo the transcription factor CG9650, the ortholog of mammalian Bcl11a/b, as a regulator of AMP proliferation predicted by our analysis. Our study demonstrates the power of time series synexpression analysis to characterize Drosophila embryonic progenitor lines and identify stem/progenitor cell regulators.

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Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization [Microarray Expression]

2015-09-23 | GSE73335 | GEO

Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization [RNA-Seq]

2015-09-24 | GSE73353 | GEO

Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization [Microarray Expression]

Project description:To characterize the sequence of events associated with RasV12 immortalization of Drosophila embryonic cells, we generated transcriptional time series during cell line establishment, from primary cultures until passage (P) 19. We generated two transcriptional time series from two cell lines (R3 and R7) by sampling the cultures at successive stages, early (P2-4), intermediate (P4-11), and late (P16-19), characterized by different passage times. Time points for the R3 time-series were: P2, P2 (replicate), P5, P6, P7, P8, P16, P17 and P19; for the R7 time-series: P2, P2 (replicate), P3, P4, P7, P8, P16, P17 and P19.

2015-09-23 | E-GEOD-73335 | biostudies-arrayexpress

Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization [RNA-Seq]

Project description:To characterize the sequence of events associated with RasV12 immortalization of Drosophila embryonic cells, we generated transcriptional time series during cell line establishment, from primary cultures until passage (P) 19. We generated three transcriptional time series from three cell lines (R1, R4 and R5) by sampling the cultures at successive stages, early (P2-4), intermediate (P4-11), and late (P16-19), characterized by different passage times. Time points for the R1 time-series were: P2, P3, P4, P5, P7, P8, P10, P11, P16, P17 and P19; for the R4 time-series: P2, P3, P4, P5, P6, P7, P9, P11, P12, P16, P17 and P19; and for the R5 time-series: P2, P3, P4, P6, P7, P8, P16, P17 and P19

2015-09-24 | E-GEOD-73353 | biostudies-arrayexpress

Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization

Project description:Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization

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Drosophila species embryonic development RAMPAGE time series

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-12-19 | GSE89335 | GEO

Histone Demethylase Lsd1 Represses Hematopoietic Stem and Progenitor Cell Signatures During Blood Cell Maturation.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Dynamic regulation of chromatin signatures during Drosophila embryonic glial differentiation

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-11-20 | GSE83377 | GEO

Discovery of signatures of fatal neonatal illness in vital signs using highly comparative time-series analysis.

Project description:To seek new signatures of illness in heart rate and oxygen saturation vital signs from Neonatal Intensive Care Unit (NICU) patients, we implemented highly comparative time-series analysis to discover features of all-cause mortality in the next 7 days. We collected 0.5 Hz heart rate and oxygen saturation vital signs of infants in the University of Virginia NICU from 2009 to 2019. We applied 4998 algorithmic operations from 11 mathematical families to random daily 10 min segments from 5957 NICU infants, 205 of whom died. We clustered the results and selected a representative from each, and examined multivariable logistic regression models. 3555 operations were usable; 20 cluster medoids held more than 81% of the information, and a multivariable model had AUC 0.83. New algorithms outperformed others: moving threshold, successive increases, surprise, and random walk. We computed provenance of the computations and constructed a software library with links to the data. We conclude that highly comparative time-series analysis revealed new vital sign measures to identify NICU patients at the highest risk of death in the next week.

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