GEO DataSets

(Submitter supplied) DNA is folded into higher-order structures that shape and are shaped by genome function. The role of long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNA Pol II) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitor cells (NPCs) and post-mitotic neurons. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

27 Samples

Download data: BROADPEAK, BW, NARROWPEAK, TSV, TXT

(Submitter supplied) The molecular basis for the female bias of systemic lupus erythematosus remains unclear. We sought to determine the fidelity of dynamic X-chromosome inactivation maintenance in the pathogenesis of murine models of spontaneous lupus, including the heavily female-biased NZM2328 model.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

11 Samples

Download data: XLS

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

Organism:

Drosophila melanogaster; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL24676 GPL22339

35 Samples

Download data

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other; Genome variation profiling by high throughput sequencing

Platforms:

GPL18573 GPL15520 GPL21290

167 Samples

Download data: XLSX

(Submitter supplied) Human embryonic stem cells (hESC) and cancer cells rapidly divide with a short G1/S-phase causing increased replicative stress (RS). Since both in vitro cultured hESCs and most high-risk neuroblastomas have large chromosome 17q gains (17q+), we hypothesize that this may provide a "RS-resistance phenotype". We co-cultured parental cells and a derived hESC line with 17q+ under normal growth conditions and under RS. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21290

115 Samples

Download data: CSV

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021

26 Samples

Download data: TXT

(Submitter supplied) Barrett’s esophagus in gastrointestinal reflux patients constitutes a columnar epithelium with distal characteristics, prone to progress to esophageal adenocarcinoma. HOX genes are known mediators of position-dependent morphology. Here we show HOX collinearity in the adult gut while Barrett’s esophagus shows high HOXA13 expression in stem cells and their progeny. HOXA13 overexpression appears sufficient to explain both the phenotype (through downregulation of the epidermal differentiation complex) and the oncogenic potential of Barrett’s esophagus. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) Knockout of the ubiquitously expressed microRNA-17~92 cluster in mice produces a lethal developmental defect and blocked B lymphopoiesis. We validated the equally widely expressed Bcl2l11 gene as joint target of miR-17~92 cluster members. Bcl2l11 encodes the pro-apoptotic protein BIM, central to life-death decisions in most mammalian cells. To study the contribution of miR-17~92:Bim interaction to miR-17~92 overall function, we set up a system of conditional mutagenesis of the Bim 3’UTR in mice. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

4 Samples

Download data: TSV

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

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platforms:

GPL13112 GPL23053

23 Samples

Download data

(Submitter supplied) Knockout of the ubiquitously expressed microRNA-17~92 cluster in mice produces a lethal developmental defect and blocked B lymphopoiesis. We validated the equally widely expressed Bcl2l11 gene as joint target of miR-17~92 cluster members. Bcl2l11 encodes the pro-apoptotic protein BIM, central to life-death decisions in most mammalian cells. To study the contribution of miR-17~92:Bim interaction to miR-17~92 overall function, we set up a system of conditional mutagenesis of the Bim 3’UTR in the mouse. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL23053

10 Samples

Download data: XLSX

(Submitter supplied) Glucocorticoid Receptor (GR) suppresses inflammation by activating anti-inflammatory and repressing pro-inflammatory genes. GR-interacting protein (GRIP)1 of the p160 family has emerged as a unique GR corepressor in macrophages (MΦ), however, whether GRIP1 contributes to GR-activated transcription, and what dictates its context-specific coactivator vs. corepressor properties is unknown. We report that loss of GRIP1 in human and mouse MΦ attenuated GR-mediated induction of several anti-inflammatory targets, revealing a non-redundant function of GRIP1 in coactivation. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL16791

21 Samples

Download data: BIGWIG

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL16570 GPL13112 GPL10787

53 Samples

Download data: BED, BIGWIG, CEL, TXT

(Submitter supplied) Igh/Myc translocations underlie both sporadic Burkitt lymphoma (BL) and the endemic clinical form affecting African children infected with malaria. However, while sporadic translocations decapitate Myc from 5' proximal regulatory elements, most endemic events occur hundreds of kilobases away from Myc. The origin of these rearrangements and how they deregulate oncogenes at such distances remain unclear. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL11002

34 Samples

Download data: TXT, WIG

(Submitter supplied) To identify key biological pathways that define toxicity or biocompatibility after nanoparticle exposure, three human cell types were exposed in vitro to two high aspect ratio nanoparticles for 1 hr or 24 hr and collected for global transcriptomics. Transcriptional responses were measured by global microarray analysis of cells in culture.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

30 Samples

Download data: CEL