GEO DataSets

(Submitter supplied) Ovarian cancer is one of the most common gynecologic malignancies globally, which is a significant cause of morbidity and mortality, accounting for 207,252 new deaths each year. The 5-year survival rate of this cancer is reported to be 26-42% and is often diagnosed in an advanced stage. Epithelial ovarian cancer (EOC) is a heterogeneous disease that comprises various histological subtypes. Of them, high-grade serous ovarian cancer (HGSOC) is the most common cancer subtype (70-80%), which is highly aggressive and grows rapidly. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

161 Samples

Download data: TXT

(Submitter supplied) There is evidence of pathophysiologic diversity in chronic rhinosinusitis with nasal polyps (CRSwNP), but data characterizing the molecular endotypes of CRSwNP and their association with treatment is lacking. The objective of this study was to identify gene signatures associated with CRSwNP endotypes, clinical features, and dupilumab treatment response. Two distinct transcriptional clusters (C1 and C2) were identified, both with elevated type 2 biomarkers. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

172 Samples

Download data: CEL

(Submitter supplied) The immunomodulatory mycobacterial surface antigen lipoarabinomannan (LAM) with its immunogenic glycan component arabinomannan (AM) facilitates Mycobacterium tuberculosis’ (Mtb) escape from the host’s immune response. Some but not all antibodies against AM can protect against TB. To better understand which of AM’s structures to target, we must first identify the spectrum of its epitopes. We here used synthetic AM oligosaccharide motifs to deplete sera from subjects along the spectrum of Mtb infection. more...

Organism:

synthetic construct; Homo sapiens

Type:

Protein profiling by protein array

Platform:

GPL34369

107 Samples

Download data: GPR, XLSX

(Submitter supplied) Authorization of the Matrix-M-adjuvanted R21 vaccine by three countries and its subsequent endorsement by the World Health Organization (WHO) for malaria prevention in children is a milestone in the fight against malaria. Yet, to meet the unprecedented demand for malarial vaccines, there is a pressing need for additional adjuvants that induce robust and durable vaccine-induced immunity. Here, we performed a comparative assessment of three clinically relevant adjuvants (an alum formulation of the TLR7/8 agonist 3M-052 (3M-052+Alum), the TLR4 agonist GLA-LSQ (GLA in liposome QS-21 formulation), and Matrix-M, the currently approved adjuvant for R21) for their capacity to induce durable immune responses to the R21 malaria vaccine in non-human primates. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32224

256 Samples

Download data: TXT

(Submitter supplied) Cyclin-dependent kinase 7 (CDK7), part of general transcription factor TFIIH, promotes gene transcription by phosphorylating the C-terminal domain of RNA polymerase II (Pol II). Here, we combine rapid CDK7 kinase inhibition with multi-omics analysis to unravel the direct functions of CDK7 in human cells. CDK7 inhibition causes Pol II retention at promoters, leading to decreased Pol II initiation and immediate global downregulation of transcript synthesis. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL21697

100 Samples

Download data: BW

(Submitter supplied) Profiling of Gln3 IDR sequence to reveal specificity determinants and their regulation

Organism:

Saccharomyces cerevisiae

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27812

327 Samples

Download data: TXT

(Submitter supplied) Epidemiological studies show that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson’s disease (PD). Animal studies support a link between developmental dieldrin exposure and increased neuronal susceptibility in the α-synuclein preformed fibril (α-syn PFF) and MPTP models in adult male C57BL/6 mice. In a previous study, we showed that developmental dieldrin exposure was associated with sex-specific changes in DNA modifications within genes related to dopaminergic neuron development and maintenance at 12 weeks of age. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24247

150 Samples

Download data: COV

(Submitter supplied) During ontogeny, γδ T cells emerge from the thymus and directly seed peripheral tissues for in situ immunity, though their functional role in humans is largely defined from blood. Here, we analyzed the phenotype, transcriptome, function, and repertoire of human γδ T cells in blood, mucosal and lymphoid tissues from 176 donors across the lifespan, revealing distinct profiles in children compared to adults. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

148 Samples

Download data: TSV

(Submitter supplied) The continued development of novel genome editors calls for a universal method to analyze their off-target effects. Here we describe a versatile method, Tracking-seq, for in situ identification of off-target effects that is broadly applicable to common genome editing tools, including Cas9, base editors, and prime editors. Through tracking RPA-bound single-stranded DNA followed by strand-specific library construction, Tracking-seq requires a low cell input and is suitable for in vitro, ex vivo, and in vivo genome editing, providing a sensitive and practical genome-wide approach for off-target detection in various scenarios. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

111 Samples

Download data: BW

(Submitter supplied) We present comprehensive epigenomic and transcriptomic mapping of 18 tumor and 20 non-neoplastic tissues from non-small cell lung adenocarcinoma patients. Our profiling covers active marks (H3K4me3, H3K4me1, and H3K27ac), repressive marks (H3K27me3 and H3K9me3) and gene expression using only 20 mg of tissue. Genome-wide differentially modified peaks and differentially expressed genes associated with non-small cell lung cancer were identified. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

442 Samples

Download data: BROADPEAK, BW, NARROWPEAK, TXT

(Submitter supplied) How parental histone H3-H4 tetramers, the primary carrier of epigenetic modifications, are transferred to leading and lagging strands of DNA replication forks following DNA replication is an important question that remains not well understood. Here we show that DNA polymerase clamp PCNA and its partner involved in lagging strand DNA synthesis, Pol d, regulate parental histone transfer to lagging strands. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

274 Samples

Download data

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL20795

112 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) SARS-CoV2 infection results in clinically heterogeneous manifestations that are partially driven by complex longitudinal interactions with the immune system. The public health burden of mild COVID-19 is massive given the >100 million infected worldwide, but most research has focused on severe and fatal COVID-19. We recruited a mild COVID-19 cohort for multimodal immunophenotyping of single immune cells (scRNAseq, scATACseq, flow cytometry), serum proteins, virus-specific cellular and humoral immune responses, and clinical annotation from early acute infection to convalescence. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL27644

201 Samples

Download data: CSV, H5, TSV

(Submitter supplied) We generated DNA methylation profiles of 500 diverse individuals to enable to construction and validation of DNA methylation biomarkers of aging.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL33022

500 Samples

Download data: CSV, IDAT

(Submitter supplied) Adult haematopoietic stem cells (HSCs) are responsible for the lifelong production of blood and immune cells and must respond to extracellular cues including cytokines. The JAK/STAT pathway is a highly conserved pathway, activated by many cytokines, in which tyrosine-phosphorylated STATs (pSTATs) function as transcription factors. STAT5 is a pivotal downstream mediator of several cytokines known to regulate haematopoiesis but its function in the HSC compartment remains poorly understood. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

288 Samples

Download data: H5AD, TXT

(Submitter supplied) Genome-wide DNA methylation profiling of normal and lung adenocarcinoma fresh tissue samples. The Illumina Infinium MethylationEPIC BeadChip (850K) was used to obtain DNA methylation profiles across 860,000 CpGs in fresh tissue of lung adenocarcinoma and adjacent histological normal lung tissue samples. Samples included 30 paired tumor-normal driver gene-negative lung adenocarcinoma tissues and 35 paired tumor-normal EGFR-mutation positive lung adenocarcinoma tissues.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

130 Samples

Download data: IDAT, TXT

(Submitter supplied) Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow samples.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL16131

172 Samples

Download data: CEL, CYCHP

(Submitter supplied) In order to study the similarities and differences in embryonic development between plant-parasitic nematodes and free-living nematodes, we performed RNA-seq on embryos of three plant-parasitic nematodes at a total of 11 stages from the single-cell stage to the J1 stage

Organism:

Heterodera glycines; Ditylenchus destructor; Meloidogyne incognita

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34498 GPL34499 GPL34500

162 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

106 Samples

Download data

(Submitter supplied) Study to map diabetes-related traits in the Diversity Outbred (DO) mouse cohort. The DO is an outbred mouse population derived from 8 inbred mouse strains, including 3 wild-derived strains. The DO captures a broad range of genetic variation comparable to that found in human populations (SVENSON et al. 2012), and presents a similarly broad range of individual susceptibility to T2D. We metabolically challenged 500 DO mice with a high-fat/high-sucrose diet, measured a host of diabetes-related physiological phenotypes (e.g., plasma glucose and insulin), and isolated their pancreatic islets for functional and molecular characterization. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

378 Samples

Download data: CSV