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Items: 1 to 20 of 1386

  • The following term was not found in GEO DataSets: Tunyasuvunakool.
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1.

Cell-specific neuropathology and multiple morphogenic mechanisms in 3D human-derived tissue

(Submitter supplied) Single-cell sequencing of donor-derived 3D cerebral organoids comparing those from schizphrenic patients to those from healthy donors.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
7 Samples
Download data: CSV
Series
Accession:
GSE184878
ID:
200184878
2.

Multi-Dimensional Epigenetic Analysis Reveals Transcription as a Primary Driver of Radiation Induced Double Strand Break Recognition

(Submitter supplied) DNA Double Strand Breaks (DSBs) are a deleterious product of genotoxic agents or radiotherapy. Despite the inherent chromatin localization of DSBs, the literature has largely ignored the effect of local chromatin or histone post translational modifications (PTMs) on DSB induction or recognition especially in a therapy-relevant setting. Analysis of epigenetic linkages to the DNA Damage Response are challenging owing to the random nature of exogenous DSB induction. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
10 Samples
Download data: BED, BIGWIG, NARROWPEAK
Series
Accession:
GSE181934
ID:
200181934
3.

Natural C. elegans microbiota protects against infection via production of a cyclic lipopeptide of the viscosin group

(Submitter supplied) Caenorhabditis elegans is associated in nature with a species-rich, distinct microbiota, which was characterized only recently. Thus, our understanding of the relevance of the microbiota for nematode fitness is still at its infancy. One major benefit that the intestinal microbiota can provide to its host is protection against pathogen infection. However, the specific strains conferring the protection and the underlying mechanisms of microbiota-mediated protection are often unclear. more...
Organism:
Caenorhabditis elegans
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13657
54 Samples
Download data: TXT
Series
Accession:
GSE136942
ID:
200136942
4.

Synthetic introns enable mutation-dependent targeting of cancer cells

(Submitter supplied) Many cancers carry recurrent change-of-function mutations in RNA splicing factor genes, which induce sequence-specific changes in RNA splicing. Here, we describe a method to harness this change in RNA splicing activity to drive splicing factor mutation-dependent gene expression in cancers and selectively eliminate these tumors. We engineered synthetic introns which were efficiently spliced in leukemia and breast epithelial cells bearing the most common SF3B1 mutations, but unspliced in wild-type cells—and vice versa—to yield mutation-dependent protein production. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL15520
28 Samples
Download data: CSV
Series
Accession:
GSE163217
ID:
200163217
5.

Single-cell RNA-seq data for control and POU IV-misexpressed Ciona intestinalis embryos at late tailbud (LTB) stage

(Submitter supplied) Purpose: Understand how the misexpression of key sensory cell determinant POU IV affects cell type specification of various sensory neurons in the peripheral nervous system in Ciona. Methods: CesA>POU IV (2.5ng/l) + CesA>GFP (5.0ng/l) injected eggs and control eggs were fertilized side by side, and allowed to develop to the late tailbud stage (13.5h after fertilization at 18°C). For each sample, 120 morphologically normal embryos were used for single cell RNA-seq assays. more...
Organism:
Ciona intestinalis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29701
2 Samples
Download data: H5
Series
Accession:
GSE192645
ID:
200192645
6.

Impact of exogenous caffeine on regulatory networks of microRNAs in response to Colletotrichum gloeosporioides in tea plant.

(Submitter supplied) Anthracnose, caused by Colletotrichum gloeosporioides is one of the most serious diseases of tea plant [Camellia sinensis (L.) O. Kuntze]. MicroRNAs are key modulators of gene expression in defense responses and plant immunity; although, foliar application of exogenous caffeine in anthracnose disease control management has proven to be effective, miRNA-mediated regulatory mechanisms underlying caffeine-induced plant defense response to C. more...
Organism:
Camellia sinensis
Type:
Other; Non-coding RNA profiling by high throughput sequencing
Platform:
GPL25554
32 Samples
Download data: XLSX
Series
Accession:
GSE146713
ID:
200146713
7.

LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer [Secondary Tuba-seq]

(Submitter supplied) Background: LKB1 is among the most frequently altered tumor suppressors in lung adenocarcinoma. Inactivation of Lkb1 accelerates the growth and progression of oncogenic KRAS-driven lung tumors in mouse models. However, the molecular mechanisms by which LKB1 constrains lung tumorigenesis and whether the aggressive cancer state that stems from Lkb1 deficiency can be reverted remains unknown. Purpose: To ascertain the tumor-suppressive capacity C/EBP family members, including Cebpa, Cebpb, and Cebpd, through CRISPR/Cas9-mediated targeting in a genetically engineered mouse model of oncogenic KRAS-driven lung adenocarcinoma. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL19057
15 Samples
Download data: TXT
Series
Accession:
GSE179499
ID:
200179499
8.

LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer [Primary Tuba-seq]

(Submitter supplied) Background: LKB1 is among the most frequently altered tumor suppressors in lung adenocarcinoma. Inactivation of Lkb1 accelerates the growth and progression of oncogenic KRAS-driven lung tumors in mouse models. However, the molecular mechanisms by which LKB1 constrains lung tumorigenesis and whether the aggressive cancer state that stems from Lkb1 deficiency can be reverted remains unknown. Purpose: To assess the impact of CRISPR/Cas9-mediated targeting of a subset of LKB1-dependent genes and C/EBP factors on tumor size in the context of a genetically engineered mouse model of oncogenic KRAS-driven lung adenocarcinoma. more...
Organism:
Mus musculus
Type:
Other
Platform:
GPL19057
24 Samples
Download data: TXT
Series
Accession:
GSE179497
ID:
200179497
9.

Growth-limiting drought stress induces time-of-day dependent transcriptome and physiological responses in hybrid poplar

(Submitter supplied) Episodic drought stress negatively impacts the health of long-lived trees. Understanding the genetic and molecular mechanisms that underpin response to drought stress is requisite for selecting or enhancing climate change resilience. Here we aim to establish standardized drought stress protocols for transcriptome studies in poplar trees, to determine how hybrid poplars respond to prolonged and uniform exposure to drought; to determine if the responses to moderate and more severe growth-limiting drought stresses were qualitatively or quantitatively different; and, to determine how response to drought changes throughout the day. more...
Organism:
Populus sp. cv. 'Okanese'
Type:
Expression profiling by high throughput sequencing
Platform:
GPL31109
18 Samples
Download data: TXT
Series
Accession:
GSE191155
ID:
200191155
10.

Multiscale profiling of enzyme activity in cancer [scRNA-seq]

(Submitter supplied) Purpose: The goal of this study was to use enzyme activity as a proxy for profiling tumor progression and treatment response in an autochthonous mouse model of Alk-mutant non-small-cell lung cancer (NSCLC). The Eml4-Alk model was originally described in Maddalo et al., Nature 2014. Single-cell transcriptomic profiling of the Eml4-Alk NSCLC model was performed for unbiased discovery of the phenotypic landscape of Eml4-Alk and wild type mice. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
2 Samples
Download data: H5
Series
Accession:
GSE191078
ID:
200191078
11.

Multiscale profiling of enzyme activity in cancer [Bulk-seq]

(Submitter supplied) Purpose: The goal of this study was to use enzyme activity as a proxy for profiling tumor progression and treatment response in an autochthonous mouse model of Alk-mutant non-small-cell lung cancer (NSCLC). The Eml4-Alk model was originally described in Maddalo et al., Nature 2014. This dataset describes bulk RNA-seq profiling of cells from Eml4-Alk lungs following administration of a protease-activatable probe, QZ1, and sorting single cells based on signal from this probe. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
8 Samples
Download data: CSV
Series
Accession:
GSE191071
ID:
200191071
12.

Dual RNA-seq on Klebsiella pneumoniae infection to human epithelial cells

(Submitter supplied) Klebsiella pneumoniae poses significant threat to global health. Detailed investigation to the nature of its interaction to human epithelial cells is still lacking. OmpR is an important regulator to the expression of major outer membrane protein genes, ompF and ompC. Here, we exploited the recently described dual RNA-seq to simultaneously measure genome-wide expression of host and pathogen two hours into infection. more...
Organism:
Klebsiella pneumoniae; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25943
5 Samples
Download data: TXT
Series
Accession:
GSE123964
ID:
200123964
13.

Cancer-associated RUNX3 missense mutation promotes the expansion of isthmus stem cells and inhibits their differentiation in the stomach II

(Submitter supplied) Background & Aims: RUNX transcription factors play pivotal roles in embryonic development and neoplasia. We previously identified the single missense mutation R122C in RUNX3 from human gastric cancer. However, how RUNX3R122C mutation disrupts stem cell homeostasis and promotes gastric carcinogenesis remained unclear. Methods: To understand the oncogenic nature of this mutation in vivo, we generated the RUNX3R122C knock-in mice. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23479
10 Samples
Download data: XLSX
Series
Accession:
GSE190506
ID:
200190506
14.

Conditional deletion of Pdcd1 identifies the cell-intrinsic action of PD-1 on functional CD8 T cell subsets for anti-tumor efficacy

(Submitter supplied) PD-1 blockade has a profound effect on the ability of the immune system to eliminate tumors but many questions remain about the cell types involved and the underlying mechanisms of immune activation. To shed some light on this, the cellular and molecular events following inhibition of PD-1 signaling was investigated in the MC-38 colon carcinoma model using constitutive (PD-1 KO) and conditional (PD1cKO) PD-1 KO mice as well as in wild type mice treated with an anti-PD-1 antibody. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
46 Samples
Download data: TXT
Series
Accession:
GSE171274
ID:
200171274
15.

Genome-wide maps of histone PTMs and co-factors in pluripotent mouse embryonic stem cells (mESCs) and epiblast-like cells (EpiLCs)

(Submitter supplied) We report here the genome wide mapping of histone PTMs and chromatin bound factors in pluripotent control and H3K27R base edited mouse embryonic stem cells (mESCs) and epiblast-like cells (EpiLCs) using ChIP-Seq technology. We have deposited results from chromatin immunoprecipitations done using antibodies against Rpb1 (Pol-II), Med1,H3.3, H3K27me1, H3K27me2, H3K27me3 and H3K27ac (rabbit and mouse monoclonal antibodies). more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
52 Samples
Download data: TXT, XLSX
Series
Accession:
GSE160974
ID:
200160974
16.

Cancer-associated RUNX3 missense mutation promotes the expansion of isthmus stem cells and inhibits their differentiation in the stomach

(Submitter supplied) Background & Aims: RUNX transcription factors play pivotal roles in embryonic development and neoplasia. We previously identified the single missense mutation R122C in RUNX3 from human gastric cancer. However, how RUNX3R122C mutation disrupts stem cell homeostasis and promotes gastric carcinogenesis remained unclear. Methods: To understand the oncogenic nature of this mutation in vivo, we generated the RUNX3R122C knock-in mice. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28457
6 Samples
Download data: XLSX
Series
Accession:
GSE190081
ID:
200190081
17.

EndoTime: Non-categorical timing estimates for endometrial tissue during the secretory phase

(Submitter supplied) It is estimated that 1% of women suffer from Recurrent Pregnancy Loss (RPL), a debilitating condition currently defined as three or more consecutive miscarriages with no known preventative treatment. However, as 65% of women are able to successfully bear children following diagnosis the risk of RPL appears to be relatively transient. The foundation for embryo implantation is the endometrium – a complex heterogenous tissue that is also transitory in nature, and which dynamically cycles between phases of proliferation, maintenance and elimination. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
108 Samples
Download data: XLSX
Series
Accession:
GSE180485
ID:
200180485
18.

Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling

(Submitter supplied) Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. more...
Organism:
Danio rerio
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL23085 GPL30372
2 Samples
Download data: BEDGRAPH, TSV
Series
Accession:
GSE179673
ID:
200179673
19.

RNA-sequencing of cells derived from dermis and postmortem dura mater from the same subject

(Submitter supplied) Patient-derived cells hold great promise for precision medicine approaches in human health. Fibroblast cells have been a major source of human cells for reprogramming and differentiating into specific cell types for disease modeling. Such cells can be isolated at various stages during life (presymptomatic, symptomatic, and advanced disease) and thus can potentially be used to model different phases of disease progression. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
8 Samples
Download data: SF
Series
Accession:
GSE178933
ID:
200178933
20.

Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RRBS]

(Submitter supplied) Heart failure can be induced or ameliorated by regulation of chromatin modifying enzymes. Because so many chromatin factors regulate gene expression, we used ATAC-seq to report the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, the majority of which persisted to the decompensated phase (3 weeks), revealing the temporal nature of epigenomic compensation to pathologic stimuli. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL24247 GPL21493
23 Samples
Download data: CGMAP
Series
Accession:
GSE154520
ID:
200154520
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