GEO DataSets

(Submitter supplied) It remains unclear how sleep influences inflammatory pathways after myocardial infarction (SF). In this study, we relied on established murine models and assessed how sleep fragmentation (SF) alters transcriptional programing in the blood, heart, and brain after MI.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34328

7 Samples

Download data: H5

(Submitter supplied) How sleep influences the transcriptional programing of blood leukocytes in humans remains incompletely undertstood. Volunteers with adequate sleep participated in a 6 week cross-over design trial. During the habitual sleep (HS) phase, participants did not alter their sleep and slept adequately. During the sleep restriction phase (SR), participants restricted their sleep by ∼1.5 hours per night. PBMCs from 8 individuals (4 HS and 4 SR) were collected subjected to scRNAseq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

32 Samples

Download data: H5

(Submitter supplied) Gastrointestinal (GI) B cells and plasma cells (PCs), critical to mucosal homeostasis, play an important role in the host response to HIV-1 infection. Here, high resolution mapping of human B cells and PCs from colon and ileum during both viremic and suppressed HIV-1 infection identified a significant reduction in germinal center (GC) B cells and Follicular Dendritic Cells (FDCs) during HIV-1 viremia. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL21697

44 Samples

Download data: RDA

(Submitter supplied) Matrix-assisted laser desorption/ionization mass spectrometry imaging allows for the study of metabolic activity in the tumor microenvironment of brain cancers. The detectable metabolites within these tumors are contingent upon the choice of matrix, deposition technique, and polarity setting. In this study, we compared the performance of three different matrices, two deposition techniques, and the use of positive and negative polarity in two different brain cancer types and across two species. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

2 Samples

Download data: TAB

(Submitter supplied) The diverse clinical outcomes of prostate cancer have led to the development of gene signature assays predicting disease progression. Improved prostate cancer progression biomarkers are needed as current RNA biomarker tests have varying success for high-risk prostate cancer. Interest grows in universal gene signatures for invasive carcinoma progression. Early breast and prostate cancers share characteristics, including hormone dependence and BRCA1/2 mutations. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL32605

51 Samples

Download data: RCC

(Submitter supplied) Transcription-coupled DNA repair (TCR) removes bulky DNA lesions impeding RNA polymerase II (RNAPII) transcription. Recent studies have outlined the stepwise assembly of TCR factors CSB, CSA, UVSSA, and TFIIH around lesion-stalled RNAPII. However, the mechanism and factors required for the transition to downstream repair steps, including RNAPII removal to provide repair proteins access to the DNA lesion, remain unclear. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

9 Samples

Download data: TXT

(Submitter supplied) Transcription-coupled DNA repair (TCR) removes bulky DNA lesions impeding RNA polymerase II (RNAPII) transcription. Recent studies have outlined the stepwise assembly of TCR factors CSB, CSA, UVSSA, and TFIIH around lesion-stalled RNAPII. However, the mechanism and factors required for the transition to downstream repair steps, including RNAPII removal to provide repair proteins access to the DNA lesion, remain unclear. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

9 Samples

Download data: TXT

(Submitter supplied) Genome-wide DNA methylation analysis (Infinium Human Methylation EPIC BeadChip platform, Illumina) performed in 24 IBCs and six normal breast tissues.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

30 Samples

Download data: IDAT

(Submitter supplied) To evaluate the miRNAs expression related to breast cancer recurrence

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL33556

23 Samples

Download data: RCC

(Submitter supplied) Purpose: HbSC disease, a less severe form of sickle cell disease, affects the retina more frequently and patients have higher rates of proliferative retinopathy that can progress to vision loss. This study aimed to identify differences in the expression of endothelial cell-derived molecules associated with pathophysiology of proliferative sickle cell retinopathy (PSCR).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: XLSX

(Submitter supplied) The ventrolateral medulla (VLM) is a crucial region in the brain for visceral and somatic control, serving as a significant source of synaptic input to the spinal cord. Experimental studies have shown that gene expression in individual VLM neurons is predictive of their function. However, the molecular and cellular organization of the VLM has remained uncertain. This study aimed to create a comprehensive dataset of VLM cells using single-cell RNA sequencing in male and female mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21626 GPL30172

16 Samples

Download data: H5

(Submitter supplied) Photoreception, a form of sensory experience, is essential for normal development of the mammalian visual system. Detecting photons during development is a prerequisite for visual system function - from shaping vision’s first synapse and maturation of retinal vascular networks, to transcriptional establishment and maturation of cell types within the visual cortex. Consistent with this theme, we find that the lighting environment regulates developmental rod photoreceptor apoptosis via OPN4-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

9 Samples

Download data: CSV

(Submitter supplied) Targeting the α4β7-MAdCAM-1 axis with vedolizumab (VDZ) is a first-line treatment in ulcerative colitis (UC). However, mechanism(s) of action (MOA) of VDZ remain relatively undefined. Here, we examined five distinct cohorts of patients with UC (n=83, n=60, n=21, n=31, n=401), to determine the effect of VDZ on the mucosal and peripheral immune system. We found a significant decrease in colonic and ileal naïve B and T cells and circulating gut- homing plasmablasts (β7+) in VDZ-treated patients, pointing to gut-associated lymphoid tissue (GALT) targeting by VDZ. more...

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: H5AD, TXT

(Submitter supplied) Klebsiella pneumoniae poses a significant global health threat primarily attributable to its pronounced resistance. Here, we report an in vitro acquired resistance analyses of K. pneumoniae to the combination of amikacin and polymyxin B. We found some differentially expressed genes associated with the resistome of K. pneumoniae. The main differences were found in the genes aphA, asmA, phoP, and in the arn operon. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32198

6 Samples

Download data: CSV

(Submitter supplied) Ischemic Stroke (IS) is one of the most impairing complications of sickle cell anemia (SCA), responsible for 20% of mortality in patients. Rheological alterations, adhesive properties of sickle reticulocytes, leukocyte adhesion, inflammation and endothelial dysfunction are related to the vasculopathy observed prior to ischemic events. The role of the vascular endothelium in this complex cascade of mechanisms is emphasized, as well as in the process of ischemia-induced repair and neovascularization. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: TXT

(Submitter supplied) Many tumor types harbor alterations in the Hippo pathway, including mesothelioma, where a high percentage of cases are considered YAP1/TEAD dependent. Identification of autopalmitoylation sites in the hydrophobic palmitate pocket of TEADs, which may be necessary for YAP1 protein interactions, has enabled modern drug discovery platforms to generate compounds that allosterically inhibit YAP1/TEAD complex formation and transcriptional activity. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

49 Samples

Download data: TXT

(Submitter supplied) The osteogenic differentiation process is essential for bone development and metabolism, but the underlying gene regulatory networks have not been well investigated. In this study, we performed RNA-seq analysis of mesenchymal stem cell differentiation to preosteoblasts and osteoblasts, derived from normal human induced pluripotent stem cell (iPSC) lines. Systematic analyses revealed potential transcription factor (TF) - TF regulatory networks, regulatory roles of long noncoding RNAs (lncRNAs), and differential splicing of extracellular matrix, TF, lncRNA, and splicing factor genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

60 Samples

Download data: TXT

(Submitter supplied) Individuals with Williams syndrome (WS), a multisystemic neurodevelopmental disorder, characteristically portray a hypersocial phenotype. WS is caused by the hemizygous loss of 26-28 genes at chromosomal locus 7q11.23, one of which is GTF2I. Copy number variations and mutations in GTF2I are associated with altered sociality and have been proposed to underlie the hypersocial expression of WS. However, the contribution of GTF2I to human neurodevelopment remains poorly understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: CSV

(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:

GPL30172 GPL24247

63 Samples

Download data: BED, BW, CSV, H5, HIC, TSV

(Submitter supplied) IL-4 activates tissue resident macrophages (TRMs) to mediate tissue repair and clearance of nematode infections in mice, but most studies have been performed on the C57BL/6 background. The natural genetic variation between C57BL/6 and BALB/c mouse strains can result in differences in allergic responses, parasite resistance, monocyte to macrophage conversion and response to IL-4 activation. Here, we investigated in vivo IL-4 activation in TRMs of the peritoneal cavity from C57BL/6 and BALB/c mice and find that C57BL/6 TRMs are surprisingly more transcriptionally responsive to IL-4 stimulation, with greater association of induced genes with super enhancers, induced enhancers and topologically associating domains (TAD) boundaries. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

5 Samples

Download data: H5