Transcriptomics (Published)

This project serves as a centralized repository for omics datasets published by research groups within the SyNergy Cluster. It encompasses investigations such as proteomics and transcriptomics, which are further divided into individual studies led by SyNergy members. Each study is linked to relevant publications, assays and data files (with links to external repositories).

To explore investigations and their associated studies in more detail, please visit the 'Related items' tab on the Project ...

Multiple sclerosis (MS) is an inflammatory neurological disease of the central nervous system with a subclinical phase preceding frank neuroinflammation. CD8+ T cells are abundant within MS lesions, but their potential role in disease pathology remains unclear. Using high-throughput single-cell RNA sequencing and single-cell T cell receptor analysis, we compared CD8+ T cell clones from the blood and cerebrospinal fluid (CSF) of monozygotic twin pairs in which the cotwin had either no or subclinical ...

Oxytocin-expressing paraventricular hypothalamic neurons (PVNOT neurons) integrate afferent signals from the gut, including cholecystokinin (CCK), to adjust whole-body energy homeostasis. However, the molecular underpinnings by which PVNOT neurons orchestrate gut-to-brain feeding control remain unclear. Here, we show that mice undergoing selective ablation of PVNOT neurons fail to reduce food intake in response to CCK and develop hyperphagic obesity on a chow diet. Notably, exposing wild-type ...

Hypothalamic astrocytes are particularly affected by energy-dense food consumption. How the anatomical location of these glial cells and their spatial molecular distribution in the arcuate nucleus of the hypothalamus (ARC) determine the cellular response to a high caloric diet remains unclear. In this study, we investigated their distinctive molecular responses following exposure to a high-fat high-sugar (HFHS) diet, specifically in the ARC. Using RNA sequencing and proteomics, we showed that ...

The bone marrow in the skull is important for shaping immune responses in the brain and meninges, but its molecular makeup among bones and relevance in human diseases remain unclear. Here, we show that the mouse skull has the most distinct transcriptomic profile compared with other bones in states of health and injury, characterized by a late-stage neutrophil phenotype. In humans, proteome analysis reveals that the skull marrow is the most distinct, with differentially expressed neutrophil-related ...

In the present study, we have demonstrated that extracellular vesicles (EVs) derived from cerebrospinal fluid (CSF) represent a promising source for the identification of a novel miRNA signatures in Parkinson's disease (PD). Using next‐generation small‐RNA sequencing, we present for the first time the complete and quantitative microRNAome of EVs isolated from human CSF of PD and age‐correlated controls (CTR). In parallel, we performed CSF proteomic profiling of overlapping patient cohorts, which ...

CD8+ T cells from PBMCs of the MS twin cohort (n = 12; 6 healthy twins, 6 twins with SCNI, and 12 twins with MS; 193,771 cells) and the validation cohort (n = 17; 5 individuals with IIH and 12 individuals with MS; 89,859 cells) were isolated via FACS and processed using the 10X manufacturer's protocol to generate single-cell transcriptome and TCR libraries. The corresponding TCR sequences are included within the metadata of the uploaded objects. (Author states that fastq raw data files from humans ...

We treated male Oxt-ires-Cre;RiboTag mice with either vehicle or CCK, collected hypothalami 2h post injection, pooled 2-3 tissues per sample, and affinity purified conditionally HA-tagged ribosomes (incl translating mRNA) specifically from oxytocin neurons. We then performed gene expression profiling analysis using data obtained from RNA-seq of immunoprecipitates versus inputs (n=4 per group) from standard chow diet fed mice and inputs only from high-fat/high-sugar diet fed mice (n=4 per group). ...

Hypothalamic oxytocin neurons from Oxt-ires-Cre;CAG-Sun1sfGFP mice were isolated by Fluorescence-activated nuclei sorting (FANS) according to the presence or absence of sfGFP signal and analyzed using snRNAseq2.

ARC tissue derived from C57BL/6JRj mice fed with SC diet (control), 5 days of HFHS (58%) diet, and 15 days of HFHS (58%) diet was dissociated by enzymatic digestion into single cells, which were then analyzed by scRNA-Seq. Per each experimental group, the ARCs from 6 animals were pulled into one sample.

C57BL/6JRj mice were exposed to a SC or a HFHS (58%) diet at 8-9 weeks of age for 4 months. Afterwards, hypothalami, hippocampi, and half cortices derived from 2 animals were isolated and pooled together in distinct tubes. A number of 5-7 replicates per each group was used. ACSA2+ astrocytes were isolated from each sample by magnetic-activated cell sorting (MACS), and further processed for RNA-Sequencing analysis.