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SRX4493020: GSM3315722: LSD1 ChIP non Wnt-Treated; Homo sapiens; ChIP-Seq
3 ILLUMINA (Illumina HiSeq 2000) runs: 105.7M spots, 10.6G bases, 3.5Gb downloads

Submitted by: NCBI (GEO)
Study: ChIP-Seq analysis for GFI1B, Beta-Catenin, LSD1 and histone marks in response to Wnt treatment
show Abstracthide Abstract
Gfi1b is a DNA binding transcriptional repressor highly expressed in hematopoietic stem cells (HSCs) and megakaryocytes (MKs). Gfi1b deficiency leads to the expansion of both cell types and abrogates the ability of MKs to respond to integrin substrates with spreading and movement. Here we show that Gfi1b is present in complexes with ²-catenin and its co-factors Pontin52, CHD8, TLE3 and CtBP1 and can regulate Wnt/²-catenin dependent gene expression. In reporter assays, Gfi1b can activate TCF-dependent transcription and this activation is enhanced upon treatment with Wnt3a. This requires the interaction between Gfi1b and lysine demethylase 1 (LSD1), but is independent of the ability of Gfi1b to bind DNA. This suggests that a tripartite ²-catenin/Gfi1b/LSD1 complex exists that regulates Wnt/²-catenin target genes. Consistently, expression of many canonical Wnt/²-catenin target genes is deregulated in Gfi1b-deficient cells and many of these target genes are co-occupied by Gfi1b, ²-catenin and LSD1 at promoter sites. When Gfi1b deficient cells were treated with Wnt3a, their normal cellularity was restored and Gfi1b-deficient MKs regained their ability to spread on integrin substrates. This suggests that Gfi1b controls both the cellularity and functional integrity of HSCs and MKs by regulating Wnt/²-catenin signaling pathway. Overall design: Chromatin immunoprecipitation was carried out in K562 cells for GFI1B, Beta-Catenin, LSD1, H3, H3K4me1, H3K9me2. ChIP was carried in both the presence and absence of Wnt3a treatment
Sample: LSD1 ChIP non Wnt-Treated
SAMN09745280 • SRS3615382 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina HiSeq 2000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: PAIRED
Construction protocol: Cells were fixed with 1% formaldehyde. Cell lysis was performed using the following buffers: total cell lysis - 5mM PIPES pH 8, 85mM KCl, 0.5% NP-40, 1X protease inhibitor cocktail, 1mM PMSF, and nuclear lysis – 50mM Tris, 10mM EDTA, 1% SDS, 1X protease inhibitor cocktail, 1mM PMSF. After sonication (Covaris E220 sonicator), immunoprecipitation was performed using Protein A/G Dynabeads (Life Technologies) For ChIP-Seq experiments, sequencing libraries were prepared from immunoprecipitated chromatin using the TruSeq DNA kit from Illumina according to the manufacturer's instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS. For RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer's instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS
Experiment attributes:
GEO Accession: GSM3315722
Links:
Runs: 3 runs, 105.7M spots, 10.6G bases, 3.5Gb
Run# of Spots# of BasesSizePublished
SRR762920635,441,1623.5G1.2Gb2019-02-21
SRR762920735,155,0233.5G1.2Gb2019-02-21
SRR762920835,094,7453.5G1.2Gb2019-02-21

ID:
6084781

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