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SRX2172851: GSM2319485: H3K9-14Ac-AB3-IPS-Fibr_F_Y-fMG02; Mus musculus; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 25.9M spots, 1.3G bases, 455.4Mb downloads

Submitted by: NCBI (GEO)
Study: The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [ChIP-Seq_Mm]
show Abstracthide Abstract
In the developing retina, as in many other regions of the central nervous system, multipotent neural progenitor cells undergo unidirectional changes to produce differentiated cells in a precise spatiotemporal order. Here we profile the epigenetic and transcriptional changes that occur during retinal development in mice and humans. Although some progenitor genes and cell cycle genes were epigenetically silenced during retinogenesis, the most dramatic change was derepression of cell type–specific differentiation programs. We identified developmental stage–specific superenhancers and showed that the majority of epigenetic changes during murine retinal development are conserved in the human retina. To determine how the epigenome changes during tumorigenesis and reprogramming, we performed the same integrated epigenetic analysis of murine and human retinoblastomas and iPSCs derived from murine rod photoreceptors. The retinoblastoma epigenome mapped to the developmental stage when retinal progenitors switch from a neurogenic to a terminal pattern of cell division and murine retinoblastomas initiate earlier in development than human tumors. The epigenome of retinoblastomas was far more similar to that of normal retina than was the epigenome of retinal-derived iPSCs but we were able to identify retinal specific epigenetic memory. Together, these data provide an in depth view of the dynamic epigenome during neurogenesis and how that relates to developmental tumors and epigenetic memory in iPSCs produced from neurons. Overall design: Examination of 8 different histone modifications and 3 transcription factors, transcriptome, DNA methylation in 23 cell types
Sample: H3K9-14Ac-AB3-IPS-Fibr_F_Y-fMG02
SAMN05785314 • SRS1700528 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 2000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: ChIP with iDeal ChIP-seq kit (Diagenode # C01010051), MinElute PCR-purification kit (QIAGEN #28006), quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies #Q33120) Libraries were prepared from 5-10 ng DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext High-Fidelity 2x PCR Master Mix according to the manufacturer’s instructions (New England Biolabs, Ipswich, MA) with the following modifications: A 1:1 Ampure cleanup was added after adaptor ligation a total of 2 times.
Experiment attributes:
GEO Accession: GSM2319485
Links:
Runs: 1 run, 25.9M spots, 1.3G bases, 455.4Mb
Run# of Spots# of BasesSizePublished
SRR425289125,867,9431.3G455.4Mb2017-05-03

ID:
3167777

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