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GSE180248 Transcriptomic analysis of HDAC6-selective and broad HDAC inhibitors in human WT iPSC cardiomyocytes
Contributors : Jin Yang ; Francis Grafton ; Ana Budan ; Sara Ranjbarvaziri ; Farshad Farshidfar ; Marie Cho ; Emma Xu ; Jaclyn Ho ; Mahnaz Maddah ; Kevin E Loewke ; Julio Medina ; David Sperandio ; Snahel Patel ; Tim Hoey ; Mohammad A MandegarSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDilated cardiomyopathy (DCM) is characterized by reduced cardiac output, as well as thinning and enlargement of left ventricular chambers. These characteristics eventually lead to heart failure. Current standards of care do not target the underlying molecular mechanisms associated with genetic forms...
Source: GEO: Gene Expression Omnibus - December 31, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE179656 Phenotypic Screening  with Deep Learning Identifies HDAC6 Inhibitors as Cardioprotective Agents in Mouse Models of Dilated Cardiomyopathy 
Contributors : Jin Yang ; Francis Grafton ; Ana Budan ; Sara Ranjbarvaziri ; Farshad Farshidfar ; Marie Cho ; Emma Xu ; Jaclyn Ho ; Mahnaz Maddah ; Kevin E Loewke ; Julio Medina ; David Sperandio ; Snahel Patel ; Tim Hoey ; Mohammad A MandegarSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDilated cardiomyopathy (DCM) is characterized by reduced cardiac output, as well as thinning and enlargement of left ventricular chambers. These characteristics eventually lead to heart failure. Current standards of care do not target the underlying molecular mechanisms associated with genetic forms...
Source: GEO: Gene Expression Omnibus - December 31, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE136193 Characterizing epigenetic effects of HISTONE DEACETYLASE 6 on DNA methylation, siRNA biogenesis and nucleosome positioning using two hda6 alleles in ros1 background
Contributors : Shoudong Zhang ; Huan Zhong ; Qianwen WangSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Arabidopsis thalianaDNA cytosine methylation is a hallmark of epigenetic gene silencing. DNA demethylation requires ROS1, a bifunctional  DNA glycosylase/lyases and open chromatin status mediated by IDM1. HDA6 is a RDP3-like histone deacetylase and was confirmed to mediate DNA methylation. In previous screening for ros1 suppressor, we identified two hda6 mutants revert...
Source: GEO: Gene Expression Omnibus - July 7, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Methylation profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE154232 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (srHC-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : OtherOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome by inducing ectopic transcription factors (TFs...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE154214 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (ChIP-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partia...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE154148 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (RNA-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome b...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE72534 Modeling genome-wide transcriptional cis-regulation in n LNCaP-abl cell line after siRNA knock down of a series of gene factors RNA-seq
We describe, MARGE, Model-based Analysis of the Regulation of Gene Expression, a robust methodology that leverages a large library of genome-wide H3K27ac ChIP-seq profiles to predict key regulated genes and cis-regulatory regions in human or mouse. MARGE adopts a gene centric approach to define a regulatory potential that summarizes the aggregate activity of multiple cis-regulatory elements on each gene. This model is effective in describing cis-regulatory activity and, unlike the super-enhancer based approach, is highly predictive of gene expression changes in response to BET-bromodomain inhibitors. We show that linear co...
Source: GEO: Gene Expression Omnibus - May 16, 2016 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research