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| Status |
Public on Jul 04, 2013 |
| Title |
Induced Cdx2 binding in progenitor motor neurons and its effect on H3K27me3 chromatin domains [ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We aim to understand the role that Cdx2 plays in specifying the rostro-caudal identity of differentiating motor neurons. We find that expressing Cdx2 in combination with FGF signaling is sufficient to produce motor neurons with a more caudal identity. ChIP-seq analysis of Cdx2 finds that it binds extensively throughout the Hox regions in progenitor motor neurons. Analysis of polycomb-associated chromatin over Hox regions in the subsequently generated motor neurons finds that Cdx2 binding corresponds to chromatin domains encompassing de-repressed caudal Hox genes. These results suggest a direct role for Cdx2 in specifying caudal motor neuron identity.
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| Overall design |
ChIP-seq studies: We characterize the binding of Cdx2 in progenitor motor neurons using a V5 tagged doxycycline inducible Cdx2 ESC line (iCdx2). Progenitor motor neurons were generated after 4 days of in vitro differentiation of mouse embryonic stem cells using retinoic acid (RA) and hedgehog (Hh) signaling exposure at day 2. On day 3, the cells are exposed to Dox with and without accompanying FGF signaling. The genome-wide binding of the induced Cdx2 transcription factor is profiled using ChIP-seq with an anti-V5 antibody. An appropriate whole-cell extract control experiment for these ChIP-seq experiments is also included.
We also examine the effect of induced Cdx2 expression on polycomb-associated chromatin structure in the resulting cellular populations by profiling the H3K27me3 chromatin mark using ChIP-seq. H3K27me3 experiments were performed after 5 days of in vitro differentiation using cells exposed to either: 1) RA & Hh to derive progenitor motor neurons, followed by Dox & FGF; 2) Dox & FGF alone; or 3) RA and Hh alone. There are 6 Illumina sequencing datasets included in this submission: two biological replicates of iCdx2 ChIP-seq in the presence of FGF; one sample of iCdx2 ChIP-seq in the absence of FGF; one H3K27me3 ChIP-seq in the presence of RA, Hh, Dox, and FGF; one H3K27me3 ChIP-seq in the presence of Dox and FGF; and one H3K27me3 ChIP-seq in the presence of RA and Hh.
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| Contributor(s) |
Mahony S, Mazzoni EO, Morrison CA, Gifford DK, Wichterle H |
| Citation(s) |
23955559 |
| Submission date |
Jul 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Shaun Mahony |
| E-mail(s) |
mahony@psu.edu
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| Phone |
814-865-3008
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| Organization name |
Penn State University
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| Department |
Biochemistry & Molecular Biology
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| Lab |
Shaun Mahony
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| Street address |
404 South Frear Bldg
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platforms (1) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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| Samples (6)
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| GSM968709 |
induced V5-tagged Cdx2 (iCdx2-V5) in RA/Hh-derived progenitor motor neurons (Day4) exposed to Dox and FGF [ChIP-Seq] |
| GSM968710 |
induced V5-tagged Cdx2 (iCdx2-V5) in RA/Hh-derived progenitor motor neurons (Day4) exposed to Dox but not FGF [ChIP-Seq] |
| GSM968711 |
H3K27me3 in Day5 cells exposed to Dox(iCdx2) and FGF [ChIP-Seq] |
| GSM968712 |
H3K27me3 in RA/Hh-derived motor neurons (Day5) exposed to Dox(iCdx2), RA, Hh and FGF [ChIP-Seq] |
| GSM968713 |
H3K27me3 in RA/Hh-derived motor neurons (Day5) exposed to RA and Hh [ChIP-Seq] |
| GSM982144 |
WCE_Day5-Seq |
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| This SubSeries is part of SuperSeries: |
| GSE39453 |
Induced Cdx2 binding in progenitor motor neurons and its effect on H3K27me3 chromatin domains |
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| Relations |
| BioProject |
PRJNA170868 |
| SRA |
SRP014444 |
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