GEO DataSets

(Submitter supplied) Many questions remain about how close association of genes and distant enhancers occurs and how this is linked to transcription activation. In erythroid cells, LDB1 is recruited to the β-globin locus via LMO2 and is required for looping of the β-globin locus control region (LCR) to the active β-globin promoter. We show that the LDB1 dimerization domain (DD) is necessary and, when fused to LMO2 is sufficient, to completely restore LCR-promoter looping and transcription in LDB1 depleted cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TXT

(Submitter supplied) During the human cord blood CD34+ cell differentiation, expression of the genes which contribute to erycyte maturation are increased, inculding ALAS2, SLC25A37, GYPA and KLF1. ETO2 functions as a transcription repressor and is required for the erythrocyte maturation and the hemoglobin switch. During mouse embryonic erythropoiesis, RNA-seq data in E8.5 yolk sac /E12.5, E14.5 fetal liver cells indicated that eto2 promoted a critical developmental transition and played an important role in globin switch from embryonic to adult β-globin transcription since its function is essential for erythorid maturation regulators (Alas2,Slc25a37,Epb42,Gypc,Klf1) and globin genes (Hbb-y and Hba-x) regulation.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL20301

30 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

100 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) To determine direct targets and the regulatory role of ETO2 in gene expression, we performed ChIPmentation with antibodies to unmodified ETO2 and ETO2 interacted factor LDB1. A de novo MEME search performed on ETO2-occupied sites, revealed enrichment for GATA and TAL binding motifs, which are the components in LDB1 complex. Nearly 86% of ETO2-binding sites were intergenic or intronic, suggesting ETO2 functions primarily in regions of the genome likely to encompass enhancers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: NARROWPEAK

(Submitter supplied) ETO2 functions as a transcription repressor and is required for the embryonic erythropoiesis and the hemoglobin switch. To gain insight into ETO2 regulatory function during human erythropoiesis, we performed RNA-seq for WT and ETO2 KO K562 cells and found that up-regulated genes upon ETO2 loss in human cells included many markers of mature erythroid cells EPB42, ALAS2, GYPA and SLC25a37. Notably, the α-globin genes (HBA1, HBA2 and HBZ) and embryonic and fetal β-globin genes (HBE1, HBG1, and HBG2) were significantly increased after deletion of ETO2. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112

64 Samples

Download data: TXT

(Submitter supplied) The Ldb1/GATA-1/TAL1/LMO2 complex mediates long range interaction between the β-globin locus control region (LCR) and gene in adult mouse erythroid cells but whether this complex mediates chromatin interactions at other developmental stages or in human cells is unknown. We investigated human NLI (Ldb1 homologue) complex occupancy and chromatin conformation of the β-globin locus in human erythroid cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13738

6 Samples

Download data: TXT

(Submitter supplied) Utilize high-throughput transcriptomic and cistromic analysis to determine the functional requirement for LDB1 and ISL1 in mature murine pancreatic β-cells while simultaneously assessing their functional interdependence at the chromatin level.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

21 Samples

Download data: BED, BW, XLSX

(Submitter supplied) We used ChIP-Seq to map Ldb1, Scl and Gata1 binding sites in mouse total bone marrow cells. Together with functional studies comparing gene expression in Murine Erythroleukemia (MEL) cells expressing Ldb1 shRNA or control shRNA and bioinformatics analysis, we systematically determined the transcriptional program controlled by Ldb1 complexes in erythropoiesis. This represents the ChIP-Seq component of the study only

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

4 Samples

Download data: BED, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL21626 GPL21103 GPL20301

90 Samples

Download data: BED, BIGWIG, NARROWPEAK, TXT

(Submitter supplied) To determine hemogen function in regulatory elements, ChIPmentation was performed in both WT and hemogen KO K562 cells and H3K27ac enrichment was significantly reduced at both promoters and enhancers in loss of hemogen. To identify direct targets and the regulatory role of hemogen in murine erythroid gene expression, hemogen and BRG1 ChIP-seq was performed in the WT and hemogen KO E14.5 fetal liver cells. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20301 GPL21103

24 Samples

Download data: BED, BIGWIG, NARROWPEAK

(Submitter supplied) To gain insight into hemogen function during human erythropoiesis, RNA-seq was performed in different type of erythroid cells, such as WT and hemogen KD CD34+ cells, WT and hemogen KD HUDEP2 cells, WT and hemogen KO K562 cells. Notably, depletion of hemogen in these human erythroid cells significantly reduced the expression of genes associated with heme and hemoglobin synthesis, such as ALAS2, HMBS, GYPA, EPOR, and HBB, supporting a positive role of hemogen in erythroid maturation. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL20301

62 Samples

Download data: TXT

(Submitter supplied) To determine hemogen function in chromatin accessbility, ATAC Seq was performed in both WT and hemogen KO mouse liver. Loss of hemogen caused generally decresed of chrmoatin accessbility on the hemogen/BRG1 binding promoter and enhancer .

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

4 Samples

Download data: BED

(Submitter supplied) LMO2 is a component of multisubunit DNA-binding transcription factor complexes that regulate gene expression in hematopoietic stem and progenitor cell development. Enforced expression of LMO2 causes leukemia by inducing hematopoietic stem cell-like features in T-cell progenitor cells, but the biochemical mechanisms of LMO2 function have not been fully elucidated. In this study we systematically dissected the LMO2/LDB1 binding interface to investigate the role of this interaction in T-cell leukemia. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

10 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL9250 GPL13112

10 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Substantial evidence supports the hypothesis that enhancers are critical regulators of cell type determination, orchestrating both positive and negative transcriptional programs; however, the basic mechanisms by which enhancers orchestrate interactions with cognate promoters during activation and repression events remain incompletely understood. Here we report the required actions of the LIM domain binding protein, LDB1/CLIM2/NLI, interacting with the enhancer binding protein, ASCL1, to mediate looping to target gene promoters and target gene regulation in corticotrope cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Substantial evidence supports the hypothesis that enhancers are critical regulators of cell type determination, orchestrating both positive and negative transcriptional programs; however, the basic mechanisms by which enhancers orchestrate interactions with cognate promoters during activation and repression events remain incompletely understood. Here we report the required actions of the LIM domain binding protein, LDB1/CLIM2/NLI, interacting with the enhancer binding protein, ASCL1, to mediate looping to target gene promoters and target gene regulation in corticotrope cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

6 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Carbonic anhydrase 1 (Car1), an early specific marker of the erythroid differentiation, has been used to distinguish fetal and adult erythroid cells since its production closely follows the γ- to β-globin transition, but the molecular mechanism underlying transcriptional regulation of Car1 is unclear. Here, we show that Car1 mRNA decreases significantly when erythroid differentiation is induced in MEL cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16368

10 Samples

Download data: CEL

(Submitter supplied) To study LDB1 function in liver cell, gene expression changes and LDB1 binding and H3K27ac modification were detected by RNA-seq and ChIP-seq.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL16791

40 Samples

Download data: BIGWIG, TXT, XLSX

(Submitter supplied) We propose that the HS2 has a role in forming a β-globin TAD by activating neighboring CTCF sites and the role is beyond typical enhancer activity.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: BIGWIG

(Submitter supplied) Background: Developmental stage-specific globin expression is a complex phenomenon that involves both trans- and cis-acting elements. While functional analyses ensuing recent genome-wide association studies have highlighted the important roles of trans-factors in regulating hemoglobin expression, these factors can not exert their functions without permissive chromatin domains. By transferring thoroughly profiled beta globin locus of undifferentiated human embryonic stem cells (hESCs) or hESC-derived erythroid cells into an adult erythroid transcriptional environment, we studied the influences of histone modifications on the globin expression decision within a fixed transcriptional environment. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6244 GPL6246

20 Samples

Download data: CEL