GEO DataSets

(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:

GPL27644 GPL24676

201 Samples

Download data: CSV, H5, TSV

(Submitter supplied) The airway epithelium is composed of diverse cell types with specialized functions that mediate homeostasis and protect against respiratory pathogens. Human airway epithelial cultures at air-liquid interface (HAE) are a physiologically relevant in vitro model of this heterogeneous tissue, enabling numerous studies of airway disease​. HAE cultures are classically derived from primary epithelial cells, the relatively limited passage capacity of which can limit experimental methods and study designs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL27644

2 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Using liver metastases from 4 colorectal cancer patients (CRC-LM), we explored one receptor: EGFR whose signaling triggers cell proliferation and is exacerbated in many tumors.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

4 Samples

Download data: H5, TAR

(Submitter supplied) Purpose: Granulomas are lumps of immune cells that can form in various organs, causing chronic inflammation and tissue destruction. While most granulomas appear histologically heterogeneous and unstructured, they have a certain resemblance of lymphoid organ formation. We thus pursued the hypothesis that granuloma formation is a highly orchestrated process that mixes and repurposes various regulatory mechanisms of normal development Methods: We performed single-cell sequencing and spatial transcriptomics on granulomas from patients diagnosed with cutaneous sarcoidosis, and we bioinformatically reconstructed their gene-regulatory networks and cell-cell interactions Results: We observed regulatory processes underlying granuloma formation that were highly conserved across individuals and followed characteristic spatial patterns. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

21 Samples

Download data: CSV

(Submitter supplied) Purpose: Granulomas are lumps of immune cells that can form in various organs, causing chronic inflammation and tissue destruction. While most granulomas appear histologically heterogeneous and unstructured, they have a certain resemblance of lymphoid organ formation. We thus pursued the hypothesis that granuloma formation is a highly orchestrated process that mixes and repurposes various regulatory mechanisms of normal development Methods: We performed single-cell sequencing and spatial transcriptomics on granulomas from patients diagnosed with cutaneous sarcoidosis, and we bioinformatically reconstructed their gene-regulatory networks and cell-cell interactions Results: We observed regulatory processes underlying granuloma formation that were highly conserved across individuals and followed characteristic spatial patterns. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

36 Samples

Download data: CSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

57 Samples

Download data

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL21145 GPL27644

51 Samples

Download data: CSV, H5, MTX, TBI, TSV, TXT

(Submitter supplied) Genome-wide gene expression profiling of hESCs undergoing neuronal differentiation at four distinct time-points. hESCs are differentiated using a novel protocol, and day 0, 7, 13 and 20 were charachterized.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

8 Samples

Download data: MTX, TSV

(Submitter supplied) Genome-wide gene expression profiling of hESCs undergoing neuronal differentiation at four distinct time-points. hESCs are differentiated using a novel protocol, and day 0, 7, 13 and 20 were charachterized.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27644

2 Samples

Download data: CSV, H5, TBI, TSV

(Submitter supplied) Genome-wide gene expression profiling of hESCs undergoing neuronal differentiation at four distinct time-points. hESCs are differentiated using a novel protocol, and day 0, 7, 13 and 20 were charachterized.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

19 Samples

Download data: CSV, TXT

(Submitter supplied) Background: Non-obstructive azoospermia (NOA) is the most severe form of male infertility. Currently known causative factors, including congenital and several acquired causes can only account for approximately 30% of NOA cases. Causes for most patients with NOA remains unclear, which were known as idiopathic NOA (iNOA). However, whether iNOA is congenital defects or acquired abnormalities is a confusing problem due to the delayed diagnosis of this frustrating situation until childbearing age. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

6 Samples

Download data: CSV

(Submitter supplied) Purpose:This study was designed to systemically characterize and compare the immunological profiles of peripheral blood from patients with VKH and healthy controls. The influence of MP, which has been the most widely prescribed GC in VKH therapy, on immune phenotypes in peripheral blood from VKH patients was also evaluated. Our investigation will offer a better understanding of the function, activation and differentiation status of the leukocyte subpopulations during autoimmune VKH and after GC therapy, and may facilitate a more specific therapeutic regimen for this particular disease, which is a major cause of visual impairment. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

21 Samples

Download data: TXT

(Submitter supplied) COVID-19, caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple-organ failure, but little is known about its pathophysiology. Here, we generated single-cell atlases of 23 lung, 16 kidney, 15 liver and 18 heart COVID-19 autopsy donor tissue samples, and spatial atlases of 14 lung donors. Integrated computational analysis uncovered substantial remodeling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of myofibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24268 GPL27644

188 Samples

Download data: CSV, H5, TXT

(Submitter supplied) RNA-seq analysis was used to investigate the transcriptional profile to reflect the changes in the parental vs engineered iPSC-derived macrophages. The RNA seq analysis provided an insight to uncover underlying mechanisms that might be triggered by perturbations in SNCA, Progranulin, and MeCP2 genes in iPSC derived macrophages. RNA seq data revealed an upregulation of 431 genes and concomitant downregulation of 276 in SNCA A53T Macrophages, an upregulation of 549 genes and concomitant downregulation of 356 in GRN R493X macrophages, an upregulation of 466 genes and concomitant downregulation of 406 genes in MeCP2HM macrophages when compared to the parental unengineered macrophages. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

8 Samples

Download data: TXT

(Submitter supplied) Pleural fibrosis is defined as an excessive deposition of extracellular matrix that results in destruction of the normal pleural tissue architecture and compromised function. There is no effective medication for this disorder. Pleural mesothelial cells (PMCs/ Met-5A) play a key role in the process of pleural fibrosis. However, the detailed mechanisms are poorly understood. In our study, firstly SRSF6 protein has a major role in pleural fibrosis progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

4 Samples

Download data: TXT

(Submitter supplied) To test whether airway epithelial and immune cells in patients with severe SARS-CoV-2 pneumonia exhibit specific gene expression signatures (namely interferon-response signature) we have performed bronchoscopy on intubated patients with severe SARS-CoV-2 pneumonia and obtained bronchial brushings.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27644 GPL29811

9 Samples

Download data: H5

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

121 Samples

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(Submitter supplied) We preformed a systems biological assessment of lower respiratory tract host immune responses and microbiome dynamics in COVD-19 patients, using bulk RNA-sequencing, single-cell RNA sequencing, and techniques, and microbiome analysis. Are focus was on differential gene expression in severe COVID-19 patients who developed ventilator associated pneumonia (VAP) during their course versus severe COVID-19 patients who did not develop VAP. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

19 Samples

Download data: CSV

(Submitter supplied) We preformed a systems biological assessment of lower respiratory tract host immune responses and microbiome dynamics in COVD-19 patients, using bulk RNA-sequencing, single-cell RNA sequencing, and techniques, and microbiome analysis. Are focus was on differential gene expression in severe COVID-19 patients who developed ventilator associated pneumonia (VAP) during their course versus severe COVID-19 patients who did not develop VAP. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27644

102 Samples

Download data: CSV

(Submitter supplied) We studied the effect of BMI1 inhibition in diffuse intrinsic pontine glioma cells (DIPG). We reported the application of chromatin immunoprecipitation sequencing for high-thoughput profiling of BMI1 and H2AK119ub in diffuse intrinsic pontine glioma cells (DIPG) in response to BMI1 inhibition. We also performed bulk RNA sequencing of DIPG cells in response to pharmacological inhibition or knockdown of BMI1. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL16791 GPL27644

30 Samples

Download data: TDF, TXT