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Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE30537: Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [mRNA profiling] GSE30538: Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [ChIP-seq] Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Marco Antonio Mendoza-Parra

PROVIDER: E-GEOD-30539 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [ChIP-seq]

Project description:Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors comprising retinoic acid (RARa,b,g) and retinoid X (RXRa,b,g) receptors. How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes is unclear. Using an RA-inducible differentiation model we defined the temporal changes in the genome-wide binding patterns of RARg and RXRa and correlated them with transcription regulation. Unexpectedly, both receptors displayed a highly dynamic binding, with different RXRa heterodimers targeting identical loci. Comparison of RARg and RXRa co-binding at RA-regulated genes identified putative RXRa-RARg target genes that were validated with subtype-selective agonists. Gene regulatory decisions during differentiation were inferred from transcription factor target gene information and temporal gene expression. This analysis revealed 6 distinct co-expression paths of which RXRa-RARg is associated with transcription activation, while Sox2 and Egr1 were predicted to regulate repression. Finally, RXRa-RARg regulatory networks were reconstructed through integration of functional co-citations. Our analysis provides a dynamic view of RA signalling during cell differentiation, reveals RA heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs. RXRa; RARg and RNA Polymerase II chromatin binding has been assessed at five time points; in addition an input control for F9 cells as well as a RXRa ChIP-seq assay from a rxra-/- ko strain has been performed.

2011-10-11 | E-GEOD-30538 | biostudies-arrayexpress

Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [mRNA profiling]

Project description:Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors comprising retinoic acid (RARa,b,g) and retinoid X (RXRa,b,g) receptors. How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes is unclear. Using an RA-inducible differentiation model we defined the temporal changes in the genome-wide binding patterns of RARg and RXRa and correlated them with transcription regulation. Unexpectedly, both receptors displayed a highly dynamic binding, with different RXRa heterodimers targeting identical loci. Comparison of RARg and RXRa co-binding at RA-regulated genes identified putative RXRa-RARg target genes that were validated with subtype-selective agonists. Gene regulatory decisions during differentiation were inferred from transcription factor target gene information and temporal gene expression. This analysis revealed 6 distinct co-expression paths of which RXRa-RARg is associated with transcription activation, while Sox2 and Egr1 were predicted to regulate repression. Finally, RXRa-RARg regulatory networks were reconstructed through integration of functional co-citations. Our analysis provides a dynamic view of RA signalling during cell differentiation, reveals RA heterodimer dynamics and promiscuity, and predicts decisions that diversify the RA signal into distinct gene-regulatory programs. Transcriptional activity in F9 cells treated with different retinoic acid receptor (RAR) agonists; like all-trans retinoic acid (ATRA), BMS961 (RARg-specific), BMS753 (RARa-specific) or BMS641(RARb-specific); has been evaluated at different time-points (2, 6, 24, 48h) and compared with that found under Ethanol-vehicle treatment conditions (48h treatment).

2011-10-10 | E-GEOD-30537 | biostudies-arrayexpress

Single-tube Linear DNA amplification (LinDA) for robust ChIP-seq

Project description:Genome-wide profiling of transcription factors based on massive parallel sequencing of immunoprecipitated chromatin (ChIP-seq) requires nanogram amounts of DNA. Here we describe a high-fidelity, single-tube linear DNA amplification method (LinDA) for ChIP-seq and reChIP-seq with picogram DNA amounts obtained from a few thousand cells. This amplification technology will facilitate global analyses of transcription-factor binding and chromatin with very small cell populations, such as stem or cancer-initiating cells. In total 5 samples were generated from the F9 teratocarcinoma cell system: mRXRa-RARg-LinDA;mRXRa_100xfold-diluted_LinDA; mRXRa(1) and two others previously described in GSE30538 (mRXRa(2): !Series_sample_id=GSM757796; mRARg : !Series_sample_id=GSM757803). In addition, 14 samples were generated from the H3396 breast cancer cell system. Those samples containing the label "LinDA" has been amplified following the Linear DNA amplification method developed by Pattabhiraman et al. ((2011), Nature Methods 8, 565-67) prior library preparation for Solexa sequencing.

2011-10-11 | E-GEOD-32332 | biostudies-arrayexpress

Project description:Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics

| PRJNA144651 | ENA

Mus musculus

Project description:Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [ChIP-seq]

| PRJNA154779 | ENA

Mus musculus

Project description:Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [mRNA profiling]

| PRJNA154777 | ENA

Transcription profiling of F9 teratocarcinoma sublines characterized by the presence or absence of the RAR gamma nuclear retinoic acid receptor treated with trans retinoic acid and the novel retinoid, ST1926

Project description:Effect of all trans retinoic acid and the novel retinoid, ST1926, on the profile of gene expression in F9 teratocarcinoma sublines characterized by the presence or absence of the RAR gamma nuclear retinoic acid receptor

2005-12-31 | E-MEXP-361 | biostudies-arrayexpress

F9 Embryonal Carcinoma cell line

Project description:Expression profile for undifferentiated F9 Embryonal Carcinoma cell line Keywords: expression profile

2008-02-27 | GSE10606 | GEO

Transcription profiling of mouse F9 embryonal carcinoma cell line

Project description:Expression profile for undifferentiated F9 Embryonal Carcinoma cell line Experiment Overall Design: 3 replicates of RNA derived from undifferentiated F9 cells

2008-04-07 | E-GEOD-10606 | biostudies-arrayexpress

Phf19 knockdown effect on F9 embryonal carcinoma cells

Project description:PCL family protein Phf19/Pcl3 is one of the accessory components of the PRC2 core complex, and Phf19 is highly expressed in murine ES cells and an ES cell-like embryonic carcinoma cell line, F9 cells. Here we performed microarray analysis of embryonal carcinoma cell line F9 following Phf19 knockdown by shRNA. Knocking down Phf19/Pcl3 in F9 embryonic cells led to derepression of numerous PRC2 direct target genes.

2012-12-20 | GSE42463 | GEO

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