GEO DataSets

(Submitter supplied) Super-enhancers (SEs) are expansive regions of genomic DNA that regulate the expression of genes involved in cell identity and cell fate. Recently, we found that distinct modules within a murine SE regulate gene expression of transcription factor Vsx2 in a developmental stage- and cell-type specific manner. In the present study, we examine the ability of these modules to drive retinal development between species. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

11 Samples

Download data: MTX, TSV

(Submitter supplied) In this experiment, 3 mice were implanted orthotopically with a patient-derived xenograft, SJRHB013759_X14. After tumor engraftment and visible nodule formation, all 3 mice underwent therapy. One mouse received vehicle control (saline), while two mice were treated with a combination of vincristine and irinotecan, to mimic salvage therapy for relapsed rhabdomyosarcoma. Sedated needle biopsies were performed before (time = 0), during therapy (time = 3, 7, and 14 days), and after recurrence.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: TXT

(Submitter supplied) Eighteen samples were obtained from 9 patients who underwent delayed resection. The purpose of this study is to identify transcriptomic shifts in samples during therapy.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: TXT

(Submitter supplied) Gene expression profile at single cell level of 17 orthotopic-patient derived xenografts from neuroblastoma samples. All xenografts were obtained through the St. Jude Childhood Solid Tumor Network (https://cstn.stjude.cloud/)

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25526

17 Samples

Download data: MTX, TSV

(Submitter supplied) We identified a novel form of caspase-independent cell death (CICD) induced by BH3-mimetics. To characterize the transcriptional changes during CICD and compare these to apoptotic changes, we performed RNA Seq analysis on SUDHL6 lymphoma cells treated with the MCL1 inhibitor S63845 in the presence or abscence of the broad spectrum caspase inhibitor zVAD.fmk.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: XLS

(Submitter supplied) Recessive dystrophic epidermolysis bullosa (RDEB) is a rare inherited skin disease characterized by defects in type VII collagen leading to a range of fibrotic pathologies resulting from skin fragility, aberrant wound healing and altered dermal fibroblast physiology. Using a novel in vitro model of fibrosis based on endogenously produced extracellular matrix, we screened an FDA-approved compound library and identified antivirals as a class of drug not previously associated with anti-fibrotic action. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: XLS

(Submitter supplied) Malaria control relies on insecticides targeting the mosquito vector, but is being increasingly compromised by insecticide resistance. Elevated expression of metabolic enzymes frequently drives resistance. In diploids, gene expression is regulated both in cis, by regulatory sequences on the same chromosome, and by trans acting factors, affecting both alleles equally. Differing levels of transcription can be caused by mutations in cis-regulatory modules, but few cis-regulatory modules controlling the expression of genes that determine insecticide resistance have been identified. more...

Organism:

Anopheles gambiae

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL25377

6 Samples

Download data: TXT

(Submitter supplied) The initiation of drug response in neuroblastoma was assessed using this genetically engineered mouse model. scRNAseq was employed to determine the heterogeneity of the initial transcriptional response to the common chemotherapeutic drug, cisplatin.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL24247

11 Samples

Download data: MTX, TSV

(Submitter supplied) The similarity of preclinical models to human neuroblastoma tumors was evaluated with scRNAseq. The 13 NB cell lines represent a cross section of disease risk, clinical subtypes, genomic alterations, and disease phenotypes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

13 Samples

Download data: MTX, TSV

(Submitter supplied) Premature birth is frequently associated with abnormal brain development, leading to brain damage, the most common being diffuse white matter injury. Perinatal neuroinflammation, which relies primarily on microglial activation, contributes to the myelination failure by affecting oligodendrocytes. To better understand the pathophysiological mechanisms involved in encephalopathy of prematurity, we took advantage of a mouse model in which systemic injections of proinflammatory interleukin-1β (IL1B) disrupt oligodendrocyte differentiation, leading to hypomyelination and cognitive deficits. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

48 Samples

Download data: TXT

(Submitter supplied) Rhabdomyosarcoma (RMS) is an aggressive pediatric cancer. Despite robust expression of myogenic regulatory factors, RMS cells are blocked in a proliferative state and do not terminally differentiate. The extent to which the skeletal muscle lineage is represented in RMS tumors and the mechanisms leading to developmental arrest, remain elusive. Here, we used single-cell RNA sequencing (scRNAseq) to resolve RMS subpopulations under basal conditions as well as under genetic perturbation of the fusion protein PAX3:FOXO1 (P3F1).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

7 Samples

Download data: RDS

(Submitter supplied) Control (cMet+ T cells less than 0.5%) and cMet-enriched (7%) T cells were activated with plate-bound anti-CD3/CD28 and gene tracription was measured

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

18 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL16791

39 Samples

Download data

(Submitter supplied) We analyzed the chromatin occupancies of active (H3K27ac and H3K4me3) and repressive (H3K27me3) histone marks in adrenergic (SH-SY5Y parental) and mesenchymal (SH-SY5Y LDK-resistant and SH-EP) neuroblastoma cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

27 Samples

Download data: BROADPEAK, BW, NARROWPEAK

(Submitter supplied) RNA-sequencing was performed on the following human neuroblastoma cell lines: Kelly, NBL-S, CHP-212, SH-SY5Y, SH-SY5Y LDK-resistant and SH-EP.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) Background: Gastrointestinal symptoms in COVID-19 patients suggests that the gut may present a viral target organ. Disease development and severity is dependent on viral interaction with two cell surface human proteins, ACE2 and TMPRSS2, and on antiviral response which may lead to systemic hyperinflammatory syndrome and multiorgan dysfunction Understanding the host response to SARS-CoV-2 infection and the pathology of the disease will be greatly enhanced by the development of appropriate animal models. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

38 Samples

Download data: TXT

(Submitter supplied) Eosinophilia is associated with various persisting inflammatory diseases and often coincides with chronic fungal infections or fungal allergy as in case of allergic bronchopulmonary aspergillosis (ABPA). However, the interactions between eosinophils and fungal pathogen leading to release of inflammatory mediators from eosinophils are poorly understood. Therefore, we established a co-culture system of mouse bone marrow derived eosinophils (BMDE) with Aspergillus fumigatus (Af) that we used in part to analyse transcriptional regulation induced by Af.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT, XLSX

(Submitter supplied) Genome sequence data results are reported from experimental and bioinfomatic work using the technique 'Bulk Segregant Analysis' to determine the genetic basis of observed resistance to the azole antifungal compound itraconazole in the opportunistic fungal pathogen Aspergillus fumigatus.

Organism:

Aspergillus fumigatus

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL31245

18 Samples

Download data: VCF

(Submitter supplied) Rhabdomyosarcoma (RMS) is the most soft tissue sarcoma of childhood and histologically mimics developing skeletal muscle. To better understand RMS, we performed single-cell RNA-seq of one embryonal subtype RMS (ERMS) and one alveolar subtype RMS (ARMS). We expanded our observations by performing single-nucleus RNA-seq of 18 patient tumors (12 ERMS, 6 ARMS). All 18 of these tumors were used to generate orthotopic patient-derived xenografts, and we performed single-cell RNA-seq of all 18 O-PDXs to compare heterogeneity between the original tumor and the patient-derived model. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL15520

64 Samples

Download data: BED, MTX, TBI, TSV, TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

5 Samples

Download data: BED, MTX, TSV