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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 10, 2017 |
| Title |
Dynamics of chromatin accessibility during TGF-beta-induced EMT of Ras-transformed mammary gland epithelial cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
This SuperSeries is composed of the SubSeries listed below.
Epithelial-mesenchymal transition (EMT) is induced by transforming growth factor (TGF)-beta stimulation and facilitates tumor progression. We here performed global mapping of accessible chromatin in the mouse mammary gland epithelial EpH4 cell line and its Ras-transformed derivative (EpRas) using formaldehyde-assisted isolation of regulatory element (FAIRE)-sequencing (seq). We also searched for differentially expressed transcription factors by RNA-seq and found that Etv4, an ETS family oncogenic transcription factor, was strongly expressed in EpRas cells. Moreover, chromatin immunoprecipitation (ChIP)-seq showed that Etv4 bound to more than one-third of the accessible chromatin regions in EpRas cells treated with TGF-beta. We found by gene ontology analysis that genes encoding extracellular proteins are the most strongly down-regulated genes by Etv4 and Etv5 siRNAs. These findings suggest a mechanism of transcriptional regulation during TGF-beta-induced EMT that involves alterations of accessible chromatin.
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| Overall design |
Refer to individual Series
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| Citation(s) |
28446749 |
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| Submission date |
May 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Daizo Koinuma |
| E-mail(s) |
d-koinuma@umin.ac.jp
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| Organization name |
University of Tokyo
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| Department |
Pathology
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| Street address |
Hongo 7-3-1, Bunkyo-ku
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| City |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
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| Platforms (1) |
| GPL18635 |
Ion Torrent Proton (Mus musculus) |
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| Samples (28)
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| GSM2385536 |
RNA-seq, EpH4, untreated, 48 h, replicate 2 |
| GSM2385537 |
RNA-seq, EpH4, TGFB treated, 48 h, replicate 1 |
| GSM2385538 |
RNA-seq, EpH4, TGFB treated, 48 h, replicate 2 |
| GSM2385539 |
RNA-seq, EpRas, untreated, 48 h, replicate 1 |
| GSM2385540 |
RNA-seq, EpRas, untreated, 48 h, replicate 2 |
| GSM2385541 |
RNA-seq, EpRas, TGFB treated, 48 h, replicate 1 |
| GSM2385542 |
RNA-seq, EpRas, TGFB treated, 48 h, replicate 2 |
| GSM2385543 |
RNA-seq, EpRas, si Negative control, 48 h |
| GSM2385544 |
RNA-seq, EpRas, si Negative control, TGFB treated, 48 h |
| GSM2385545 |
RNA-seq, EpRas, si Etv4_1 and Etv5_1, 48 h |
| GSM2385546 |
RNA-seq, EpRas, si Etv4_1 and Etv5_1, TGFB treated, 48 h |
| GSM2385547 |
RNA-seq, EpRas, si Etv4_2 and Etv5_2, 48 h |
| GSM2385548 |
RNA-seq, EpRas, si Etv4_2 and Etv5_2, TGFB treated, 48 h |
| GSM2385549 |
FAIRE-seq, EpH4, untreated, 8 days, replicate 1 |
| GSM2385550 |
FAIRE-seq, EpH4, untreated, 8 days, replicate 2 |
| GSM2385551 |
FAIRE-seq, EpH4, TGFB treated, 8 days, replicate 1 |
| GSM2385552 |
FAIRE-seq, EpH4, TGFB treated, 8 days, replicate 2 |
| GSM2385553 |
FAIRE-seq, EpRas, untreated, 8 days, replicate 1 |
| GSM2385554 |
FAIRE-seq, EpRas, untreated, 8 days, replicate 2 |
| GSM2385555 |
FAIRE-seq, EpRas, TGFB treated, 8 days, replicate 1 |
| GSM2385556 |
FAIRE-seq, EpRas, TGFB treated, 8 days, replicate 2 |
| GSM2492639 |
FAIRE-seq, EpRas, siControl, untreated, 4 days |
| GSM2492640 |
FAIRE-seq, EpRas, siControl, TGF-beta treated, 4 days |
| GSM2492641 |
FAIRE-seq, EpRas, siEtv4/5 set 1, TGF-beta treated, 4 days |
| GSM2492642 |
FAIRE-seq, EpRas, siEtv4/5 set 2, TGF-beta treated, 4 days |
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| This SuperSeries is composed of the following SubSeries:
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| GSE69363 |
RNA-sequencing of EpH4 and EpRas cells treated with Etv4 and Etv5 siRNAs and/or TGF-beta. |
| GSE69364 |
Dynamics of chromatin accessibility during TGF-beta-induced EMT of Ras-transformed mammary gland epithelial cells [FAIRE-Seq] |
| GSE89618 |
Etv4 and Etv5 binding sites in EpRas mouse mammary gland epithelial cell line [ChIP-seq] |
| GSE94977 |
FAIRE-seq analysis of Ras transformed mouse mammary gland epithelial cells transfected with Etv4 and Etv5 siRNAs and stimulated with TGF-beta. |
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| Relations |
| BioProject |
PRJNA285342 |
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