GEO DataSets

(Submitter supplied) Dysfunction of epigenetic modulators such as the SWI/SNF complex is involved in a wide spectrum of cancer entities, yet their precise role in carcinogenesis is not clear to date Among SWI/SNF-mutant entities, SMARCB1-deficient cancers such as Epithelioid Sarcoma (EpS) are characterized by this genetic event in an otherwise rather silent mutational landscape. However, its oncogenic role remains unclear. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: BED

(Submitter supplied) In this study we analysed the dynamic changes in the epigenetic landscape during first embryonic lineage decision following pluripotency exit. Here, mouse pluripotent epiblast cells segregate towards mesoderm and endoderm (ME) or neuroectoderm (NE). The analysis of chromatin accessibility, histone modifications and accompanied gene expression confirmed a bias of the epigenetic landscape towards NE fate while ME cis regulatory elements (CREs) are becoming accessible and active during lineage specification. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

40 Samples

Download data: BIGWIG

(Submitter supplied) In this study we analysed the dynamic changes in the epigenetic landscape during first embryonic lineage decision following pluripotency exit. Here, mouse pluripotent epiblast cells segregate towards mesoderm and endoderm (ME) or neuroectoderm (NE). The analysis of chromatin accessibility, histone modifications and accompanied gene expression confirmed a bias of the epigenetic landscape towards NE fate while ME cis regulatory elements (CREs) are becoming accessible and active during lineage specification. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

49 Samples

Download data: TAB, XLSX

(Submitter supplied) In this study we analysed the dynamic changes in the epigenetic landscape during first embryonic lineage decision following pluripotency exit. Here, mouse pluripotent epiblast cells segregate towards mesoderm and endoderm (ME) or neuroectoderm (NE). The analysis of chromatin accessibility, histone modifications and accompanied gene expression confirmed a bias of the epigenetic landscape towards NE fate while ME cis regulatory elements (CREs) are becoming accessible and active during lineage specification. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

30 Samples

Download data: BIGWIG

(Submitter supplied) Gene expression variation results from numerous sources including genetic, environmental, life stage, and even the environment experienced by previous generations. While the importance of each has been demonstrated in diverse organisms, their relative contributions remain understudied because few investigations have simultaneously determined each within a single experiment. Here we quantified genome-wide gene expression traits in Drosophila, quantified the contribution of multiple different sources of trait variation and determined the molecular mechanisms underlying observed variation. more...

Organism:

Drosophila sechellia; Drosophila simulans; Drosophila simulans x Drosophila sechellia

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL35057 GPL35058 GPL35056

72 Samples

Download data: XLSX

(Submitter supplied) Cancer progression is associated with genetic and epigenetic aberrations that affect chromatin 3D organization in the nucleus. Changes in loop extrusion or phase separation alter the relationships between enhancer and promoter elements, defining novel gene expression programs that are selected to promote growth and survival. Here, we provide an integrative approach based on chromatin conformation, accessibility and transcription, further validated by CRISPR interference screenings in order to identify chromatin topologies relevant to different subtypes of T-cell leukemia, namely T-ALL and ETP-ALL. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

7 Samples

Download data: BED, MTX, TSV

(Submitter supplied) The histone variant H3.3 facilitates mRNA transcription activation and suppression at cis-regulatory elements such as promoters and enhancers, with histone epigenetic modifications including acetylation or methylation as context-defining features. Canonical histone H3 and histone variant H3.3 are post-translationally modified with the genomic distribution of these marks denoting transcription features and with more recent evidence suggesting that these modifications may influence transcription. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

28 Samples

Download data: BED, BW

(Submitter supplied) The histone variant H3.3 facilitates mRNA transcription activation and suppression at cis-regulatory elements such as promoters and enhancers, with histone epigenetic modifications including acetylation or methylation as context-defining features. Canonical histone H3 and histone variant H3.3 are post-translationally modified with the genomic distribution of these marks denoting transcription features and with more recent evidence suggesting that these modifications may influence transcription. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

8 Samples

Download data: BW, TXT

(Submitter supplied) Differential expression analysis of scRNA-seq data is central for characterizing how experimental factors affect the distribution of gene expression. However, distinguishing between biological and technical sources of cell-cell variability and assessing the statistical significance of quantitative comparisons between cell groups remains challenging. Here, we introduce memento, a tool designed to address these limitations by providing statistically robust and computationally efficient differential expression analysis of the mean, variability, and gene correlation from scRNA-seq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

24 Samples

Download data: CSV, H5AD

(Submitter supplied) Oncogenes can be activated in cis through multiple mechanisms including enhancer hijacking events and noncoding mutations that create enhancers or promoters de novo. These paradigms have helped parse somatic variation of noncoding cancer genomes, thereby providing a rationale to identify noncanonical mechanisms of gene activation. Here we describe a novel mechanism of oncogene activation whereby focal copy number loss of an intronic element within the FTO gene leads to aberrant expression of IRX3, an oncogene in T cell acute lymphoblastic leukemia (T-ALL). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30173

3 Samples

Download data: TDF

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

Organism:

Mus musculus; Mus

Type:

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

Platforms:

GPL23693 GPL24247

25 Samples

Download data: SF

(Submitter supplied) Natural selection has shaped the gene regulatory networks that orchestrate the development of the neocortex, leading to diverse neocortical structure and function across mammals, but the molecular and cellular mechanisms driving phenotypic changes have proven difficult to characterize. Here, we develop a reproducible protocol to generate cortical organoids from mouse epiblast stem cells that enable in depth mechanistic studies of cortical developmental in vitro. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

7 Samples

Download data: H5

(Submitter supplied) To examine the ways in which gene expression varies in natural populations and its relationship to genetic divergence, we estimated allele-specific expression in the offspring of multiple wild C. elegans strains crossed with the laboratory reference strain N2. Allele-specific expression analyses are uniquely sensitively able to identify cis regulatory changes, and coupled with analyses of differential expression between parental strains and parents and offspring can determine the regulatory pattern and inheritance mode of gene expression across the genome. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34645

45 Samples

Download data: COUNTS, SF, TSV, TXT

(Submitter supplied) Kidney organoids derived from human iPSCs have cell heterogeneity of maturation. We used single-cell RNA sequencing (scRNAs-seq) to extract the factor related to proximal tubule maturation. Using the kidney organoids cultured with the factors that accelerate the maturation speed of proximal tubules extracted by the aforementioned method, we examined whether the maturity of the proximal tubules increases within the same induction period.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

7 Samples

Download data: MTX, TSV

(Submitter supplied) Cellular transcription enables cells to adapt to various stimuli and maintain homeostasis. Transcription factors bind to transcription response elements (TREs) in gene promoters, initiating transcription. Synthetic promoters, derived from natural TREs, can be engineered to control exogenous gene expression using endogenous transcription machinery. This technology has found extensive use in biological research for applications including reporter gene assays, biomarker development, and programming synthetic circuits in living cells. more...

Organism:

Mus musculus; Homo sapiens; Mesocricetus auratus; synthetic construct

Type:

Expression profiling by high throughput sequencing

5 related Platforms

65 Samples

Download data: CSV

(Submitter supplied) The effects of genetic variation on complex traits act mainly through changes in gene regulation. Although many genetic variants have been linked to target genes in cis, the trans-regulatory cascade mediating their effects remains largely uncharacterized. Mapping trans-regulators based on natural genetic variation, including eQTL mapping, has been challenging due to small effects. Experimental perturbation approaches offer a complementary and powerful approach to mapping trans-regulators. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

215 Samples

Download data: TXT

(Submitter supplied) Roquin proteins target specific RNA stem-loop motifs with their unique ROQ domain for mRNA degradation. The cellular levels of mRNAs are controlled by these post-transcriptional cis-regulatory stem-loop elements in the 3'-untranslated region (3'-UTR). Here, we first provide an RBNS (RNA Bind-n-Seq) experiment using pre-structured RNA libraries as input. This sRBNS (structured RBNS) was used to map Roquin's RNA binding preferences at nucleotide resolution, revealing preferences for loop sizes and consensus motifs for CDEs and ADEs.

Organism:

synthetic construct

Type:

Other

Platform:

GPL27484

10 Samples

Download data: XLSX

(Submitter supplied) Establishment and maintenance of spermatogenesis need a complex process and vast regulatory network. There is growing evidence reveals that long noncoding RNAs (lncRNA) plays important role in regulating testicular development and spermatogenesis in a stage-specific way. We here report the identification of lncRNA LOC108635509 as key lncRNA regulator in black goat spermatogenesis. In the current study, we screened the transcriptomes (lncRNA and mRNA) of testicular from Guangxi black goats before puberty (3 days old, D3; 30 days old, D30), puberty (90 days old, D90) and postpuberty (180 days old, D180), and found there were 1211, 12180, 834 differential lncRNAs and 1196, 8838,269 differential mRNAs at the ages of D30 vs D3, D90 vs D30, and D180 vs D90. more...

Organism:

Capra hircus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34862

12 Samples

Download data: CSV

(Submitter supplied) The spatiotemporal configuration of genes with distal regulatory elements is believed to be crucial for transcriptional control, but full mechanistic understanding is lacking. We combine simultaneous live tracking of pairs of genomic loci and nascent transcripts with molecular dynamics simulations to assess the Sox2 gene and its enhancer. We find that both loci exhibit more constrained mobility than control sequences due to stalled cohesin at CTCF sites. more...

Organism:

Mus musculus musculus x Mus musculus castaneus

Type:

Other

Platform:

GPL31871

13 Samples

Download data: CIS

(Submitter supplied) Cytokines of the IL-6 family, such as IL-11, may influence angiogenesis. Our experiments showed opposite angiogenic effects on HUVECs depending on cis- or transsignaling of IL-11. Spheroids from the 3D angiogenesis model (spheroid sprouting assay) were lysed in QIAzole buffer by vigorous vortexing. The transcriptomic changes were analyzed by RNA sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

12 Samples

Download data: TXT