GEO DataSets

(Submitter supplied) The opioid epidemic has received considerable attention, but the impact on perinatal opioid-exposed (POE) offspring remains underexplored. This study addresses the emerging public health challenge of understanding and treating POE children. We examine two scenarios using preclinical models: offspring exposed to oxycodone (OXY) in utero (IUO) and postnatally (PNO). We hypothesized exposure to OXY during pregnancy primes offspring for neurodevelopmental deficits and severity of deficits is dependent on timing of exposure. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25947

12 Samples

Download data: TXT

(Submitter supplied) Thousands of protein domains encoded in the human genome function by binding up to a million short linear motifs embedded in intrinsically disordered regions of other proteins. How affinity and specificity are encoded in these binding domains and the motifs themselves is not well understood. The evolvability of binding specificity - how rapidly and extensively it can change upon mutation - is also largely unexplored, as is the contribution of ‘fuzzy’ dynamic residues to affinity and specificity in protein-protein interactions. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

32 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. As the light sensing part of the visual system, the human retina is composed of five classes of neuron, including photoreceptors, horizontal cells, amacrine, bipolar, and retinal ganglion cells. Each class of neuron can be further classified into subgroups with the abundance varying three orders of magnitude. Therefore, to capture all cell types in the retina and generate a complete single cell reference atlas, it is essential to scale up from currently published single cell profiling studies to improve the sensitivity. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

81 Samples

Download data: H5

(Submitter supplied) Long-term reconstituting haematopoietic stem cells (LT-HSCs) are used to treat blood disorders via allogeneic stem cell transplantation (alloSCT), to engraft and repopulate the blood system. The very low abundance of LT-HSCs and their rapid differentiation during in vitro culture hinders their clinical utility. Previous developments using stromal feeder layers, defined media cocktails, and bioengineering have enabled HSC expansion in culture, but of mostly short-term HSCs (ST-HSC) and progenitor populations at the expense of naïve LT-HSCs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

27 Samples

Download data: CSV

(Submitter supplied) Is the transcriptome of cumulus cells a good predictor of the embryo’s developmental competence? The objective of this study was to analyze the transcriptional differences between cumulus cells from oocytes exhibiting different developmental potentials following individual in vitro embryo production and transfer by RNA‐seq. Cumulus cells were allocated into three groups according to the developmental potential of their enclosed oocyte: (1) not able to develop to the blastocyst stage (Bl–), (2) able to develop to the blastocyst stage but failing to establish a pregnancy (P–), or (3) able to develop to the blastocyst stage and to establish a clinical pregnancy (P+).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

15 Samples

Download data: TSV

(Submitter supplied) We specifically deleted Mettl14 in mouse uterus using the Pgr-Cre driver. To portray the molecular mechanism for Mettl14 function in mouse uterus, uterine tissues were collected from Mettl14f/f and Mettl14d/d mice on gestational day 4 and subjected to single-cell RNA-seq analysis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: MTX, TSV

(Submitter supplied) Exosomes are nanosized extracellular vesicles with lipid bilayer membranes and contain various contents, including lipids, miRNAs and proteins, all of which are widely involved in signaling pathways and genetic information processes. Exosomes derived from adipose tissues (AT-Exos) have been identified as a crucialmedium in the transmission of information from adipose tissue to itself and to other organs, including exosomes derived from inguinal white adipose tissue (iWAT-Exos), visceral white adipose tissue (vWAT-Exos) and brown adipose tissue (BAT-Exos). more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: XLSX

(Submitter supplied) Exosomes derived from adipose tissues (AT-Exos) have been identified as a crucialmedium in the transmission of information from adipose tissue to itself and to other organs, including exosomes derived from inguinal white adipose tissue (iWAT-Exos), visceral white adipose tissue (vWAT-Exos) and brown adipose tissue (BAT-Exos). However, the functional differences in depot-specific AT-Exos under obese conditions remain elusive. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

7 Samples

Download data: XLSX

(Submitter supplied) Limb expression 1-like protein (LIX1L) plays important role in various liver disorders, but its role and underlying mechanism in nonalcoholic hepatitis (NASH) and HCC progression remains obscure. Here, we report that LIX1L functions as a key integrative regulator linking lipid metabolism and inflammation, adipose tissue dysfunction and hepatic microenvironment reprogramming which promotes NASH progression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: XLS

(Submitter supplied) Fish skeletal muscle plays a crucial role in various physiological functions, and providing an important source of meat for human consumption. Therefore, understanding the molecular genetic regulation of muscle development and growth can benefit in enhancing the efficacy of aquaculture. Morphological and skeletal muscle histological analysis of Megalobrama amblycephala at 14 development stages ranging from 5-240 days post-hatching (d) revealed that 30 d and 45 d are the crucial stages for postembryonic muscle fibers hyperplasia and hypertrophy in M. more...

Organism:

Megalobrama amblycephala

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34391

2 Samples

Download data: MTX, TSV

(Submitter supplied) Intratumoral heterogeneity (ITH) and tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) play important roles in tumor evolution and patient outcomes. However, the precise characterization of diverse cell populations and their crosstalk associated with PDAC progression and metastasis is still challenging. We performed single-cell RNA sequencing (scRNA-seq) of treatment-naive primary PDAC samples with and without paired liver metastasis samples to understand the interplay between ITH and TME in the PDAC evolution and its clinical associations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

218 Samples

Download data: TXT

(Submitter supplied) Lung adenocarcinoma is a malignant tumor with high morbidity and mortality. ZBTB16 plays a double role in various tumors; however, the potential mechanism of ZBTB16 in the pathophysiology of lung adenocarcinoma has yet to be elucidated. We herein observed a decreased expression of ZBTB16 mRNA and protein in lung adenocarcinoma and a significantly increased DNA methylation level of ZBTB16 in patients with lung adenocarcinoma. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: BW

(Submitter supplied) We explored functional redundancy of three structurally related KCTD proteins, KCTD2, KCTD5 and KCTD17 by progressively knocking them out in HEK 293 cells using CRISPR/Cas9 genome editing. After validating knockout, we assessed the effects of progressive knockout on cell growth and gene expression. We noted progressive effects of knockout of KCTD isoforms on cell growth were most pervasive when all three isoforms were deleted suggesting some functions were conserved between them. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV

(Submitter supplied) Streptococcus agalactiae is among the few pathogens that have not developed resistance to ß-lactam antibiotics despite decades of clinical use. The molecular basis of this long-lasting susceptibility has not been investigated, and it is uncertain whether specific mechanisms constraint the emergence of resistance. In this study, we first report a conserved role of the signaling nucleotide cyclic-di-AMP in the sensitivity of S. more...

Organism:

Streptococcus agalactiae; Streptococcus agalactiae NEM316

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29157 GPL34325

18 Samples

Download data: TXT

(Submitter supplied) Some individuals show a discrepancy between cognition and the amount of neuropathological changes characteristic for Alzheimer’s disease (AD). This phenomenon has been referred to as ‘resilience’. The molecular and cellular underpinnings of resilience remain poorly understood. To obtain an unbiased understanding of the molecular changes underlying resilience, we investigated global changes in gene expression in the superior frontal gyrus of a cohort of cognitively and pathologically well-defined AD patients, resilient individuals and age-matched controls (n=11-12 per group). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

35 Samples

Download data: TXT

(Submitter supplied) TP53-mutant blood cancers remain a major clinical challenge. BH3-mimetic drugs inhibit BCL-2 pro-survival proteins to promote cancer cell apoptosis. Despite acting downstream of TP53, functional TP53 is required for maximal cancer cell killing by BH3-mimetics through an unknown mechanism. Here, we report TP53 can be activated following BH3-mimetic induced mitochondrial outer membrane permeabilization, which leads to induction of BH3-only proteins, thereby potentiating the pro-apoptotic signal. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

28 Samples

Download data: TXT

(Submitter supplied) Hypertrophic cardiomyopathy (HCM) constitutes the most common genetic cardiac disorder. However, current pharmacotherapeutics are mainly symptomatic and only partially address underlying molecular mechanisms. Circular RNAs (circRNAs) are a recently discovered class of non-coding RNAs and emerged as specific and powerful regulators of cellular functions. By performing global circRNA-specific next generation sequencing in cardiac tissue of patients with hypertrophic cardiomyopathy compared to healthy donors, we identified circZFPM2 (hsa_circ_0003380. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34284

6 Samples

Download data: CSV

(Submitter supplied) Alternative RNA splicing is an essential and dynamic process in neuronal differentiation and synapse maturation, and dysregulation of this process has been associated with neurodegenerative diseases. Recent studies have revealed the importance of RNA-binding proteins in the regulation of neuronal splicing programs. However, the molecular mechanisms involved in the control of these splicing regulators are still unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23479

6 Samples

Download data: CSV

(Submitter supplied) In this study, we employed an inducible CRISPRi human induced pluripotent stem cell (hiPSC) line to silence TERT expression enabling the generation of hiPSCs and hiPSC-derived cardiomyocytes with long and short telomeres. Reduced telomerase activity and shorter telomere lengths of hiPSCs strongly hampered their differentiation potential towards cardiomyocytes

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: CSV

(Submitter supplied) Thlaspi arvense (Pennycress) is an emerging feedstock for biofuel production because of its high seed oil content enriched in erucic acid. A transcriptomic and a lipidomic study were performed to analyze the dynamics of gene expression, glycerolipid content and acyl-group distribution during seed maturation. Genes involved in fatty acid biosynthesis were expressed at the early stages of seed maturation. more...

Organism:

Thlaspi arvense

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34226

10 Samples

Download data: XLSX