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SRX6437849: GSM3940112: Junb_input_ChIP; Mus musculus; ChIP-Seq
1 ILLUMINA (Illumina HiSeq X Ten) run: 26.6M spots, 8G bases, 3Gb downloads

Submitted by: NCBI (GEO)
Study: Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis [ChIP-seq]
show Abstracthide Abstract
Oncogenes are highly specific in the cells they can transform, although the molecular basis for this is poorly understood. Inflammation often promotes tumorigenesis, and in the pancreas it promotes cellular plasticity and accelerates Kras-driven neoplasia. We demonstrate that plasticity is coupled to the emergence of transient progenitor cells that are readily transformed by KrasG12D. The progenitor state is linked to coordinate upregulation of proliferation genes through chromatin opening at nearby lineage-specific enhancers. Mutant Kras taps into this program by co-opting the normally transient enhancer elements, making them permanent and Kras-dependent in cancer. Mechanistically, co-option occurs through cooperation of Kras-driven transcription factors with the existing landscape of pancreatic lineage transcription factors, which are recruited to play a central role in driving the mutant Kras-dependent transcriptional program. These observations suggest that proliferation is controlled by tissue-specific enhancer networks that are tapped into by oncogenes, helping explain the lineage specificity of cancer drivers. Overall design: Examination of [1] 2 different histone modifications and 4 different transcription factors in PDA cell line. [2] H3K27ac histone modifications in two different types of PDA cell line by using MEK inhibitors or AKT inhibitor treatment. [3] Klf5 and Foxa2 in PDA cell line by Junb and Fosl1 overexpression .
Sample: Junb_input_ChIP
SAMN12264422 • SRS5092564 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq X Ten
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: PAIRED
Construction protocol: Briefly, cells were crosslinked at room temperature for 10 min with 1% formaldehyde, washed twice with PBS and sonicated in lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 0.1% Na-Deoxycholate, 1% Triton X-100, 1 mM EDTA, complete protease inhibitor cocktail). Samples were immunoprecipitated at 4 ºC overnight and washed six times with ChIP wash buffer (20 mM Tris, pH 7.9, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) and once with TE buffer. Bound DNA was eluted in 1% SDS buffer and reverse-crosslinked for 6 h at 65 ºC DNA samples were treated sequentially with RNase A and Protease K and then purified with ChIP DNA Clean & Concentrator-5 (Zymo Research, D4014)
Experiment attributes:
GEO Accession: GSM3940112
Links:
Runs: 1 run, 26.6M spots, 8G bases, 3Gb
Run# of Spots# of BasesSizePublished
SRR967754926,568,1898G3Gb2020-07-12

ID:
8529297

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