GEO DataSets

(Submitter supplied) Throughout evolution, the duplication and functional divergence of transcription factors (TFs) has driven cellular and organismal complexity. Mechanisms by which paralogous TFs functionally diverge are thus of broad interest yet remain poorly understood. One well-established mechanism underlying TF divergence is the occupation and regulation of distinct sets of genes. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two representative members of the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of plant TFs. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30821

48 Samples

Download data: TAB

(Submitter supplied) Throughout evolution, the duplication and functional divergence of transcription factors (TFs) has driven cellular and organismal complexity. Mechanisms by which paralogous TFs functionally diverge are thus of broad interest yet remain poorly understood. One well-established mechanism underlying TF divergence is the occupation and regulation of distinct sets of genes. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two representative members of the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of plant TFs. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24270

31 Samples

Download data: BIGWIG

(Submitter supplied) Memory B cells (MBCs) formed over the individual’s lifetime constitute nearly half of the adult peripheral blood B cell repertoire in humans. To assess their response to novel antigens, we tracked the origin and followed the differentiation paths of MBCs in the early anti-S response to mRNA vaccination in SARS-CoV-2-naïve individuals on single-cell and monoclonal antibody level. Newly generated and pre-existing MBCs differed in their differentiation paths despite similar levels of SARS-CoV-2 and common corona virus S-reactivity. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

24 Samples

Download data: CSV, H5, TXT

(Submitter supplied) SARS-CoV-2 spike (S) specific T-cell and antibody (AB) responses after primary BNT162b2 vaccination (Pfizer Inc., New York, NY, USA and BioNTech SE, Mainz, Germany) partially depend on the phenotypic composition of pre-existing T-helper (Th) cell populations (Saggau et al., 2022, Immunity). However, adaptive cellular responses and their impact on sustained immune protection after booster vaccination are incompletely understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL33412

24 Samples

Download data: RCC

(Submitter supplied) Collagen, a critical component of the tumor microenvironment (TME), significantly influences cancer-associated fibrosis, tissue stiffness, immune response, and metastasis. Pancreatic ductal adenocarcinoma (PDAC) is characterized by excessive collagen deposition, and effective therapies remain limited. Our research challenges conventional understanding by highlighting the remarkable ability of specific tumor epithelial populations, particularly those with low levels of L1 cell adhesion molecule (L1CAM) expression (L1low), to actively modulate collagen dynamics within the TME. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) In addition to their intrinsic rewarding properties. opioids can also evoke aversive reactions that protect against misuse. Cellular mechanisms that govern the interplay between opioid reward and aversion are poorly understood. We used whole-brain activity mapping to show that neurons in the dorsal peduncular nucleus (DPn) are highly responsive to the opioid oxycodone. Connectomic profiling revealed that DPn neurons innervate the parabrachial nucleus (PBn). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: H5

(Submitter supplied) The exact role of epigenetics in the pathogenesis of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is unclear. Herein we have hypothesized that viral micro RNAs (miRNAs) may modulate host cellular and immune responses which may lead to varied clinical presentations. Using bioinformatics tools, we have first predicted putative miRNAs in the genotype of the SARS-CoV-2 and their potential gene targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL33371

12 Samples

Download data: TXT

(Submitter supplied) The exact role of epigenetics in the pathogenesis of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is unclear. Herein we have hypothesized that viral micro RNAs (miRNAs) may modulate host cellular and immune responses which may lead to varied clinical presentations. Using bioinformatics tools, we have first predicted putative miRNAs in the genotype of the SARS-CoV-2 and their potential gene targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL33370

57 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; Other

Platforms:

GPL18573 GPL24676

117 Samples

Download data: ZIP

(Submitter supplied) Adult inflammatory bowel disease is incompletely understood. We combine unbiased single-cell RNA sequencing (gene expression profiling, CITE-seq derived cell surface protein data, TCR and BCR sequence data) with unbiased spatial transcriptomics to interrogate changes across immune and non-immune populations in colitis and health, across tissue and blood. We compare idiopathic ulcerative colitis with hitherto under-studied immune checkpoint therapy induced colitis, utilizing non-inflamed disease states as additional controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

16 Samples

Download data: ZIP

(Submitter supplied) The ΔcrcZ mutant shows constitutive repression of all crc/Hfq target genes in the translation. Therefore, it presents a hyper‐repressed phenotype (more repressed than the parental strain) in the acquisition of secondary carbon sources, even though the preferred carbon source is not present. Δcrc is more sensitive to antibiotics, more susceptible to oxidative stress, and less motile than the parental strain. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15987

11 Samples

Download data: TXT

(Submitter supplied) Cumulus-oocyte complexes were collected post-PMSG/hCG induction at J4 for 3 genotypes : wild-type (WT), DKO for LXRalpha and LXRbeta (DKO) and DKO for LXRalpha and LXRbeta rescued for LXRbeta in granulosa cells (TG-AMHb). Corona radiata cells were isolated from oocytes using hyaluronidase treatment and collected for transcriptomic analysis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

9 Samples

Download data: TXT

(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

Platforms:

GPL21103 GPL24247

27 Samples

Download data: BED

(Submitter supplied) In our preliminary in-vitro studies in primary neurons, we found that changing glucose utlization using 2-deoxyglucose (2-DG, a known glycolytic inhibitor, which inhibits glucose utilization) led to a dose dependent signficant increase in Bdnf gene expression. Additionally, the dose of 2-DG that induced Bdnf gene expression also normalized learning and memory in mouse model of AD (5xFAD mouse) and improved functional recovery in mice models of ischemic and hemorrhagic strokes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

9 Samples

Download data: XLSX

(Submitter supplied) Intermittent fasting (IF) has broad beneficial effects on brain pathophysiology. Here, we sought to identify the target required for beneficial effects of IF using its pharmacological mimic, 2-deoxyglucose (2-DG), which could also eliminate limitations of human IF application due to dosage and schedule issues. 2-DG transcriptionally induced plasticity gene, Bdnf in vitro and in vivo. A 2-DG dose that induced Bdnf transcription in vivo also normalized hippocampal long-term potentiation and memory in an AD mouse model (5xFAD) and significantly improved functional recovery in stroke models. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

18 Samples

Download data: BED

(Submitter supplied) Reactivation of toxoplasmosis poses a significant health risk to chronically infected people especially those with compromised immune systems. Molecular studies of reactivation have been difficult due to the lack of accurate models of bradyzoite recrudescence, which initiates disease reactivation. Here, we performed single cell RNA-sequencing (scRNA-seq) on parasite populations that form after bradyzoite infection of two host-cell types: primary mouse astrocytes and human foreskin fibroblasts. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26742

6 Samples

Download data: MTX, TSV

(Submitter supplied) Within the brain, a pro-inflammatory response is essential to prevent clinical disease due to Toxoplasma gondii reactivation. Infection in the immunocompromised leads to lethal Toxoplasmic encephalitis while in the immunocompetent, there is persistent low-grade inflammation which is devoid of clinical symptoms. T cells are the dominant immune cell that prevent clinical disease, and this is mediated through the secretion of effector molecules such as perforins and IFNγ. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: MTX, TSV

(Submitter supplied) The transcription factors MECOM, PAX8, SOX17 and WT1 are candidate master regulators of high-grade serous ‘ovarian’ cancer (HGSC), yet their cooperative role in the hypothesized tissue of origin, the fallopian tube secretory epithelium (FTSEC) is unknown. We generated 26 epigenome (CUT&TAG, CUT&RUN, ATAC-seq and HiC) data sets and 24 profiles of RNA-seq transcription factor knock-down followed by RNA sequencing in FTSEC and HGSC models to define binding sites and gene sets regulated by these factors in cis and trans. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL18573

26 Samples

Download data: BED, BEDGRAPH, BW, NARROWPEAK

(Submitter supplied) NOT PROVIDED; REQUESTED

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

30 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to analyze transcriptome profiles with RNA sequencing (RNA-seq) in metaphase II horse oocytes after vitrification before and after in vitro maturation (IVM). To do so, transcriptome profile of three groups were compared: (1) oocytes vitrified immature, warmed, and in vitro matured (VGV), (2) in vitro matured and vitrified (VMAT), and (3) fresh oocytes (CONTROL).

Organism:

Equus caballus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21401

12 Samples

Download data: CSV