GEO DataSets

(Submitter supplied) Rationale: Changes in peripheral blood cell populations have been observed but not detailed at single-cell resolution in idiopathic pulmonary fibrosis (IPF). Objectives: To provide an atlas of the changes in the peripheral immune system in stable and progressive IPF. Methods: Peripheral blood mononuclear cells (PBMCs) from IPF patients and controls were profiled using 10x Chromium 5’ single-cell RNA sequencing (scRNA-seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

38 Samples

Download data: MTX, TSV

(Submitter supplied) Our study aims to elucidate the role of lncRNA-mRNA regulatory networks in AF recurrence after catheter ablation. We performed RNA sequencing to profile the transcriptomes of 5 samples from atrial fibrillation recurrence and 5 samples from sinus rhythm maintenance. 96 differentially expressed genes (DEGs) and 203 differentially expressed long non-coding RNAs (DE-lncRNAs) were identified between atrial fibrillation recurrence group and sinus rhythm maintenance group. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of samples with/without chronic or acute Temporomandibular Disorders (TMD). The Illumina Infinium Human methylationEPIC Beadchip was used to obtain DNA methylation profiles across 1,051,943 CpGs in TMD samples. Samples included 452 non-TMD and 496 chronic TMD from OPPERA I, 36 healthy and 123 acute TMD from OPPERA II.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

1107 Samples

Download data: CSV, IDAT

(Submitter supplied) Group 3 innate lymphoid cells (ILC3s) are abundant in the developing or healthy intestine to critically support tissue homeostasis in response to microbial cues and other environmental signals. However, during gastrointestinal disease including infections, colorectal cancer, or inflammatory bowel disease (IBD), intestinal ILC3 numbers are dramatically reduced and the remaining ILC3s become dysfunctional which fuels disease and barrier breakdown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

14 Samples

Download data: TXT

(Submitter supplied) To determine gene expression changes that contribute to the development of COPD among smokers using high-throughput RNA sequencing in the peripheral blood of COPD patients. Total RNA sequencing was investigated by prospectively collecting lung function test results and whole blood samples from smokers who visited the outpatient department of respiratory medicine at three hospitals since 2020. This study confirmed gene expression differences in non-coding RNA in COPD patients according to the degree of airflow limitation through RNA-Seq transcriptome analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL30209

294 Samples

Download data: TXT

(Submitter supplied) Transcriptomic subtyping holds promise for personalized therapy in extensive stage small cell lung cancer (ES-SCLC). In this study, we aimed to assess intratumoral transcriptomic subtype diversity and to identify biomarkers associated with long-term chemoimmunotherapy benefit in human ES-SCLC. Our work highlights that high intratumoral heterogeneity, lack of consistent association with outcome, and unclear subtype-specific target expression are major challenges for SCLC subtype-based precision oncology. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL30173

175 Samples

Download data: DCC, PKC, PNG, XLSX

(Submitter supplied) Transcriptomic subtyping holds promise for personalized therapy in extensive stage small cell lung cancer (ES-SCLC). In this study, we aimed to assess intratumoral transcriptomic subtype diversity and to identify biomarkers associated with long-term chemoimmunotherapy benefit in human ES-SCLC. Our work highlights that high intratumoral heterogeneity, lack of consistent association with outcome, and unclear subtype-specific target expression are major challenges for SCLC subtype-based precision oncology. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL30173

121 Samples

Download data: DCC, PKC, PNG, XLSX

(Submitter supplied) Spermatozoa harbor a complex and environment sensitive pool of small non-coding RNAs (sncRNA)1, which influences offspring development and adult phenotypes1-7. Whether spermatozoa in the epididymis are directly susceptible to environmental cues is not fully understood8. We used two distinct paradigms of preconception acute high fat diet to dissect epididymal vs testicular contributions to the sperm sncRNA pool and offspring health. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL17021 GPL24676 GPL24247

307 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Spermatozoa deliver a complex and environment sensitive pool of small non-coding RNAs (sncRNA) to the oocyte at fertilisation, which influences offspring development and adult phenotypic trajectories. Whether mature spermatozoa in the epididymis can directly sense the environment is still not fully understood. Here, we used two distinct paradigms of preconception acute High Fat Diet challenge to dissect epididymal vs spermatogenic contributions to the sperm sncRNA pool and offspring health. more...

Organism:

Homo sapiens; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

44 Samples

Download data: TXT

(Submitter supplied) Plasmatic microRNA sequencing was conducted in specific matched subgroups of subjects (n = 53) with and without OSA using HTG EdgeSeq miRNA WTA Assay technology.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

53 Samples

Download data: TXT

(Submitter supplied) Trained immunity is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, diets, or metabolites, altering their responses to future exposures. Trained immunity is observed in hypercholesterolemia, dislipidemia, and in response to high fat diet. In this study monocytes from obese adolescents and controls were exposed to microbial stimulation in vitro or media alone, and transcriptional profiles were generated.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

22 Samples

Download data: TXT

(Submitter supplied) RNA-Seq analysis was carried out to investigate the effects of CDK8/19 inactivation in the tumors formed in intact and castrated NSG mice by different 22Rv1 derivatives, with or without SNX631 treatment. The 22Rv1 derivatives were generated as following: Parental 22Rv1 (Rv1-WT) were transduced with a lentivirus expressing luciferase, yielding the derivative Rv1-Luc. 22Rv1 cells with a double knockout of CDK8 and CDK19 (Rv1-dKO) were made via CRISPR/Cas9. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL24676

66 Samples

Download data: TXT

(Submitter supplied) DNA methylation analysis was performed for buccal samples from children exposed in utero to maternal smoking during pregnancy (with or without vitamin C supplementation) and in a smaller number of non-smoker controls

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

359 Samples

Download data: IDAT, TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

9 Samples

Download data: MTX, TSV

(Submitter supplied) Precision medicine's potential to transform complex autoimmune-disease treatment is often challenged by limited data availability and inadequate sample size when compared to the number of molecular features found in high-throughput multi-omics datasets. Addressing this issue, the novel framework PRoBeNet (Predictive Response Biomarkers using Network medicine) was developed. ProBeNet operates under the hypothesis that the therapeutic effect of a drug propagates through a protein–protein interaction network to reverse disease states. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV

(Submitter supplied) Six-week old Fah−/−/Rag2−/−/Il2rg −/− (FRG) –NOD breeding mice were intravenously injected with 1.5 x 10^9 plaque forming units (pfu) of an adenoviral vector encoding the secreted form of the human urokinase-like plasminogen activator (Ad-uPA). Forty-eight hours later, 10^6 PHH were injected intrasplenically. Successfully transplanted mice were fed with CDA-HFD for 16 weeks and then treated with humanized CLDN1 specific mAb 500 µg or vehicle for additional 8 weeks. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25431

10 Samples

Download data: TSV

(Submitter supplied) Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, and is even more in women. EGFR mutations and ALK fusions are major alterations observed in NSLA. We have focused on NSLA without EGFR and ALK alteration (NENA) rather than NSLA with EGFR and ALK (EA). First, we selected 141 NSLA tissues, and performed proteogenomic analyses including the whole-genome sequencing (WGS), transcriptome, methylation EPIC array, total proteome and phosphoproteome. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

141 Samples

Download data: IDAT, TXT

(Submitter supplied) Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, and is even more in women. EGFR mutations and ALK fusions are major alterations observed in NSLA. We have focused on NSLA without EGFR and ALK alteration (NENA) rather than NSLA with EGFR and ALK (EA). First, we selected 141 NSLA tissues, and performed proteogenomic analyses including the whole-genome sequencing (WGS), transcriptome, methylation EPIC array, total proteome and phosphoproteome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

141 Samples

Download data: TAB

(Submitter supplied) RNAseq analysis of placental gene expression in samples obtained from 59 smokers (enrolled in the VCSIP RCT: NCT03203603) and 20 never-smokers for reference.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

79 Samples

Download data: CSV

(Submitter supplied) Some people with obesity are resistant to the adverse metabolic effects of excess adiposity and are considered to have “metabolically healthy obesity” (MHO). However, the mechanisms responsible for MHO are not clear. We performed comprehensive cardiometabolic profiling in 20 adults with MHO (defined by features of normal insulin sensitivity), 20 age-, sex-, and BMI-matched adults with metabolically unhealthy obesity (MUO), and 15 adults who were metabolically healthy and lean (MHL). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

50 Samples

Download data: TXT