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Links from GEO DataSets

Items: 20

1.

Expression Data from E16.5 hearts from WT and FOG-2R3K5A siblings

(Submitter supplied) Heart development is modulated by FOG-2/NuRD interactions. FOG-2R3K5A is unable to recuit the NuRD complex and this results in cardiac defects such as ASD, VSD, and thin ventricular walls We used microarrays to detail the changes in gene expression in FOG-2R3K5A hearts to determine misexpression of genes that may be causing the observed phenotypes.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
6 Samples
Download data: CEL
Series
Accession:
GSE50426
ID:
200050426
2.

GATA4 is a direct activator of Cyclin D2 and is required for proliferation in 2nd heart field-derived myocardium

(Submitter supplied) The second heart field (SHF) comprises a population of mesodermal progenitor cells that are added to the nascent linear heart to give rise to the majority of the right ventricle, interventricular septum, and outflow tract of mammals and birds. The zinc finger transcription factor GATA4 functions as an integral member of the cardiac transcription factor network in the SHF and its derivatives. In addition to its role in cardiac differentiation, GATA4 is also required for cardiomyocyte replication, although the transcriptional targets of GATA4 required for proliferation have not been previously identified. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
11 Samples
Download data: CEL
Series
Accession:
GSE9652
ID:
200009652
3.

The Gene Expression Analysis in E12.5 Mouse Hearts with GATA4-FOG2 Interaction Loss

(Submitter supplied) In order to identify the targets of GATA4-FOG2 action in mammalian heart development we performed Affymetrix microarray comparisons of gene expression in normal and mutant at embryonic (E) day E12.5 hearts. We compared RNA samples from both Fog2-null and Gata4ki/ki mutant E12.5 hearts to the wild-type control E12.5 hearts. We reasoned that as the phenotypes of the Fog2 knockout and Gata4ki/ki mutation (a V217G mutation that specifically cripples the interaction between GATA4 and FOG proteins) are similar, we should expect to identify a similar set of differentially expressed genes in both experiments. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
6 Samples
Download data: CEL, CHP
Series
Accession:
GSE14906
ID:
200014906
4.

Transcriptome of E9.5 WT and Smyd1-KO mouse hearts

(Submitter supplied) Purpose: The goal of this study is to identify the differential cardiac transcriptome profiling between WT and Smyd1 null (Smyd1-KO) hearts at E9.5 using RNA-seq. Methods: mRNA profiles of E9.5 WT and Smyd1-KO mouse hearts were generated by deep sequencing, n=3 for each genotype, using Illumina HiSeq2500. The sequence reads were aligned to the mm10 reference genome using STAR via the bcbio-nextgen RNA-sequencing pipeline. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
6 Samples
Download data: TXT
Series
Accession:
GSE260692
ID:
200260692
5.

ATAC-seq of E9.5 WT and Smyd1-KO mouse hearts

(Submitter supplied) Purpose: The goal of this study is to identify the differential cardiac chromatin accessibility between WT and Smyd1 null (Smyd1-KO) hearts at E9.5 using ATAC-seq. Methods: Four hearts at E9.5 were pooled per genotype per replicate, and were then dissociated into single cells. 40,000 viable cells were taken for were lysed to isolate nuclei, which were treated with Tn5 transposase (Nextera DNA Sample Prep Kit, Illumina) to isolate DNA. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
4 Samples
Download data: BED, BIGWIG
Series
Accession:
GSE260690
ID:
200260690
6.

ATAC-seq of E10.5 WT and Chd4-CMko mouse hearts

(Submitter supplied) Purpose: The goal of this study is to identify the differential cardiac chromatin accessibility between WT and cardiomyocyte conditional knockout (Chd4-CMko) hearts at E10.5 using ATAC-seq. Methods: Three hearts at E10.5 were pooled per genotype per replicate, and were then dissociated into single cells. 40,000 viable cells were taken for were lysed to isolate nuclei, which were treated with Tn5 transposase (Nextera DNA Sample Prep Kit, Illumina) to isolate DNA. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24247
8 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE260689
ID:
200260689
7.

HOP homeobox (Hopx) and Histone deacetylase-2 (Hdac2) deficiency effect on the embryonic heart

(Submitter supplied) Analysis of heart ventricles from Hopx, Hdac2, and both Hopx-Hdac2 deficient embryos at embryonic day E16.5. Results provide insight into the role of Hopx and Hdac2 in cardiac development. We used microarrays to detail the global programme of gene expression underlying cardiogenesis by Hopx and Hdac2 and identified distinct classes of up-regulated and down-regulated genes during this process.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
12 Samples
Download data: CEL, CHP
Series
Accession:
GSE23700
ID:
200023700
8.

Expression data from Fog1+/+ and Fog1 ki/ki mouse megakaryocyte-erythroid progenitors (MEP).

(Submitter supplied) The transcription co-factor FOG1 interacts with the chromatin remodeling complex NuRD to mediate gene activation and gene repression during hematopoiesis. We have generated mice with a targeted mutation in the endogenous Fog1 locus that results in an N-ternimal mutation in FOG1 that disrupts the interaction with NuRD. We used gene expression microarrays to explore the global transcriptional programs regulated by FOG1 and NuRD in megakaryocyte-erythroid progenitors (MEP) to aid in understanding its role during hematopoiesis.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
6 Samples
Download data: CEL
Series
Accession:
GSE19497
ID:
200019497
9.

Expression data from TCF19 knockdown in HepG2 cells maintained under high glucose (40mM) condition

(Submitter supplied) Changes in concentration of glucose in the cellular environment results in a variety of changes in the transcription program. Liver is the primary organ for metabolic regulation in the body, and hence, any surge in circulating blood glucose leads to changes in transcriptional states of important enzymes tasked to maintain metabolic homeostasis. Chromatin modification reader proteins play an important role in maintaining metabolic homeostasis by identification of the histone modification, and facilitating recruitment of chromatin remodelling enzymes. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL15207
4 Samples
Download data: CEL
Series
Accession:
GSE107471
ID:
200107471
10.

Ush regulates macrophage-specific gene expression, fatty acid metabolism and cell cycle progression and cooperates with dNuRD to orchestrate hematopoiesis

(Submitter supplied) The generation and modulation of lineage-specific gene expression programmes that determine proliferation capacity, metabolic profile and cell type-specific activities at each stage of differentiation are crucial for metazoan development. Gene expression programmes are moulded by a complex interplay between sequence-specific transcription factors, cofactors and epigenetic regulators. Here, we study U-shaped (Ush), a genetically defined transcriptional cofactor that cooperates with GATA transcription factors during blood cell differentiation in Drosophila. more...
Organism:
Drosophila melanogaster
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19951
21 Samples
Download data: BIGWIG, TXT
Series
Accession:
GSE146382
ID:
200146382
11.

Identification of genes regulated by REST in developing hearts

(Submitter supplied) Selective suppression of cardiac gene expression by RE-1 silencing transcription factor (REST) in embryonic stage is essential for cardiogenesis and function; however, the underlying mechanism remains unclear. In this study, we show that REST  suppression of cardiac genes during development is temporarily regulated through non-CpG methylation at REST binding sites. Gene expression analyses revealed that the expression of Hcn2 (hyperpolarization-activated cyclic nucleotide-gated ion channel 2), a REST-targeted gene, was developmentally upregulated, while DNMT3B level and REST expression was downregulated. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
6 Samples
Download data: TXT
Series
Accession:
GSE80378
ID:
200080378
12.

P15 Rat Sciatic Nerve ChIP-Chip with NuRD complex components

(Submitter supplied) The NuRD complex is required for efficient and timely myelination in the peripheral nervous system. ChIP-chip assays were performed on rat sciatic nerve at P15, a peak timepoint of myelination, for binding of Chd4 to genes involved in regulating myelin formation. This experiment includes two custom ChIP-chip design incorporating many genes that are dynamically regulated during myelination. The antibodies used in this platform were Chd3/4 (Santa Cruz sc-11378) Chd4 (gift from Paul Wade), Mta2 (Santa Cruz sc-9447), and Nab2 (Santa Cruz sc-22815).
Organism:
Rattus norvegicus
Type:
Genome binding/occupancy profiling by genome tiling array
Platforms:
GPL13963 GPL10812
4 Samples
Download data: GFF, PAIR
Series
Accession:
GSE30890
ID:
200030890
13.

An ES cell–specific NuRD complex functions through interaction with Wdr5

(Submitter supplied) The Nucleosome Remodeling and Deacetylase (NuRD) complex is a chromatin regulatory complex that functions as a transcriptional co-repressor in metazoans. The NuRD subunit Mbd3 is essential for targeting and assembly of a functional NuRD complex as well as embryonic stem cell (ESC) pluripotency. Three Mbd3 isoforms (Mbd3a, Mbd3b, and Mbd3c) are expressed in mouse. Here, we find that the Mbd3c isoform contains a unique 50–amino acid N-terminal region that is necessary for Mbd3c to specifically interact with the histone H3 binding protein Wdr5. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
10 Samples
Download data: BEDGRAPH, TXT
Series
Accession:
GSE80708
ID:
200080708
14.

SetD8 Knockdown in ß-estradiol-treated (24 h) G1E-ER-GATA-1 cells

(Submitter supplied) The establishment and maintenance of cell type-specific transcriptional programs require an ensemble of broadly expressed chromatin remodeling and modifying enzymes. Many questions remain unanswered regarding the contributions of these enzymes to specialized genetic networks that control critical processes such as lineage commitment and cellular differentiation. We have been addressing this problem in the context of erythrocyte development driven by the transcription factor GATA-1 and its coregulator Friend of GATA-1 (FOG-1). more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL13912
6 Samples
Download data: TXT
Series
Accession:
GSE49174
ID:
200049174
15.

Mi2ß knockdown in ß-estradiol-treated (24 h) G1E-ER-GATA-1 cells

(Submitter supplied) Objective: To determine the extent to which GATA-1 utilizes Mi2ß to regulate gene transcription in the context of G1E-ER-GATA-1 cells.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL13912
6 Samples
Download data: TXT
Series
Accession:
GSE48188
ID:
200048188
16.

High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [WGBS]

(Submitter supplied) Reprogramming of somatic cells to induced pluripotent stem cells provoke immense interest both for clinical applications in regenerative medicine, and in understanding the regulation of cell identity. Previous characterization of the molecular events that underlie this process were limited by the low yield and by the stochastic dynamics of this process. Here we present an in-depth mapping of the molecular events that underlie an efficient and successful reprogramming, covering transcriptional, epigenetic and translational changes in a single day resolution.
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL17021 GPL19057
19 Samples
Download data: TAB
Series
Accession:
GSE104283
ID:
200104283
17.

High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [ATAC-Seq]

(Submitter supplied) Reprogramming of somatic cells to induced pluripotent stem cells provoke immense interest both for clinical applications in regenerative medicine, and in understanding the regulation of cell identity. Previous characterization of the molecular events that underlie this process were limited by the low yield and by the stochastic dynamics of this process. Here we present an in-depth mapping of the molecular events that underlie an efficient and successful reprogramming, covering transcriptional, epigenetic and translational changes in a single day resolution.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL17021 GPL19057
16 Samples
Download data: TXT
Series
Accession:
GSE103821
ID:
200103821
18.

High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
4 related Platforms
243 Samples
Download data: BED, TAB, TXT
Series
Accession:
GSE102518
ID:
200102518
19.

High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [ChIP-Seq]

(Submitter supplied) Reprogramming of somatic cells to induced pluripotent stem cells provoke immense interest both for clinical applications in regenerative medicine, and in understanding the regulation of cell identity. Previous characterization of the molecular events that underlie this process were limited by the low yield and by the stochastic dynamics of this process. Here we present an in-depth mapping of the molecular events that underlie an efficient and successful reprogramming, covering transcriptional, epigenetic and translational changes in a single day resolution.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL13112 GPL17021 GPL19057
144 Samples
Download data: BED, TXT
Series
Accession:
GSE102517
ID:
200102517
20.

High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [RNA-Seq]

(Submitter supplied) Reprogramming of somatic cells to induced pluripotent stem cells provoke immense interest both for clinical applications in regenerative medicine, and in understanding the regulation of cell identity. Previous characterization of the molecular events that underlie this process were limited by the low yield and by the stochastic dynamics of this process. Here we present an in-depth mapping of the molecular events that underlie an efficient and successful reprogramming, covering transcriptional, epigenetic and translational changes in a single day resolution.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19057 GPL17021
43 Samples
Download data: TXT
Series
Accession:
GSE102348
ID:
200102348
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