GEO DataSets

(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:

Mus musculus; Homo sapiens

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

(Submitter supplied) Perform RNAseq with existing frozen mouse DO tissues from ~500 DO mice were sensitized on a HFHS diet (Keller, Gatti et al. 2018). The same mice have been extensively characterized for T2D-relevant clinical phenotypes, ex-vivo islet function, and other features including microbiome profiling. Gene expression and proteomic profiling has already been completed in islets. We will collect and analyze the genetic architecture of gene expression in liver, adipose, heart, skeletal muscle. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

482 Samples

Download data: CSV

(Submitter supplied) Knowing when a person was infected with Mycobacterium tuberculosis (M.tb) is critical as recent infection is the strongest clinical risk factor for progression to TB disease in immunocompetent individuals. However, time since M.tb infection is very difficult to determine in routine clinical practice. We determined whether DNA methylation patterns in the blood correlate with time since M.tb infection or exposure to develop a biomarker for recent exposure. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24247

151 Samples

Download data: BEDGRAPH

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL28457 GPL24247

245 Samples

Download data

(Submitter supplied) Upon differentiation chromatin rewires in order to reflect its new cellular identity and function. Zfp608 locus is rewired following the differentiation from the ESCs to the NPCs. During this process the local chromatin content is remodelled with activating marks littering the region, local 3D chromatin conformation compacts the region through local chromatin contacts and the Zfp608 expression amplifies. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28457

189 Samples

Download data: BIGWIG

(Submitter supplied) Single Embryo Repli-Seq was utilized to investigate the replication timing in zygotes and 2-cell cleavage stage embryos. The aim was to understand the temporal progression of DNA replication during the early stages of embryonic development in mammals.

Organism:

Mus musculus

Type:

Other

Platforms:

GPL21626 GPL19057

127 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) In this study, we build an in-depth multi-omics profile of 5 Arabidopsis accessions, in order to find the inner relations of N deficit, mild drought, and combined stress response at the physiological, metabolic and transcriptional level.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19580

119 Samples

Download data: TSV