RNA-seq

Build a statistically rigorous RNA-seq analysis in R and Bioconductor. The workshop develops data import and visualisation skills, hypothesis testing and genomic interval analysis before covering read mapping, count normalisation, differential expression and multiple-testing correction. Practical comparisons include DESeq2, edgeR and limma/voom. The final session interprets functional pathways using overrepresentation and permutation-based gene-set enrichment analysis. Six live online sessions on 2, 3, 5, 6, 9 and 10 November, 15:00–18:00 Europe/Berlin (CET). Fee €530. Basic R programming and

…by phylogenetics, phylogenomics, RNA-seq processing and differential expression. Examples compare Illumina, Nanopore and PacBio data across biological systems and experimental designs. Live online, 8–12 February, 14:00–20:00 Europe/Berlin (C

Study gene regulation by processing and integrating RNA-seq, ATAC-seq, MNase-seq, ChIP-seq and Hi-C measurements. The five workshop days cover expression analysis, chromatin accessibility, chromatin composition, three-dimensional genome interactions and multi-omics integration. Practical work includes quality control, alignment, differential expression, peak and motif analysis, and visualisation of genomic contacts. Reproducible Linux and R notebooks connect assay design to biological interpretation. Live online, 22–26 February, 13:00–19:00 Europe/Berlin (CET). Fee €480. Participants need a b

…Participants study RNA-seq quantification and differential expression, protein identification and quantification, annotation and statistical evaluation. Software training includes SearchGUI, PeptideShaker and DiaNN; Cytoscape is used to integrate measurements and explore complementary information about gene and protein expression. The course connects p

This practical school introduces bulk RNA-seq analysis for biologists and data analysts with little computing experience. Participants work through Linux commands, sequencing technologies and file formats, quality assessment and trimming, read alignment, mapping diagnostics and visualization using an Illumina dataset. Later sessions compare methods for quantifying transcripts and detecting differential gene expression, splicing and isoform expression, with R graphics and exercises to interpret the results. Single-cell RNA-seq analysis is outside the programme. Teaching runs from 09:00 to 17:0

In response to chronic stress, mammalian vestibular hair cells (HC) may undergo extrusion from the sensory epithelium. Before HC loss begins, the early damage is characterized by synaptic uncoupling and dismantlement of the calyceal junction, the cell adhesion complex formed between type I HCs and calyx afferents. This early pathology associates with the early loss of vestibular function, and both the initial epithelial and functional alterations are reversible. This study was aimed at identifying key gene expression responses associated with these phenomena. We used three animal models of chr

…a mouse model of SCI, we performed RNA-seq analysis on RN isolated from con

In 2019, a report by world stroke organisation (WSO) states that there are 12.2 million new cases of ischaemic stroke per year with 6.5 million people dying annually. Stroke is the third nationally and second globally highest in terms of mortality and third highest worldwide in terms of Disability Adjusted Life Years (DALYs). Chronic ischaemia, constituting 62% of all stroke cases; and cognitive impairment are reported to be 50% associated in patients younger than 50 years, foisting a huge burden on their families. Post stroke cognitive impairment (PSCI) includes the damages caused to the cogn

…Further RNA-seq analys

Study objective was to evaluate whether seizure-inducing chemoconvulsants could induce dysregulation of non-coding RNAs (ncRNAs), similar to epileptogenic brain insults and seizures observed in-vivo.Rat primary cortical cultures were exposed to 11 chemoconvulsants (4-aminopyridine, amoxapine, bicuculline, chlorpromazine, donepezil, kainic acid, pentylenetetrazol, picrotoxin, pilocarpine HCl, SNC80, strychnine HCl) for 24 h, followed by extraction of RNA for sequencing. Salmon tool quantified ncRNAs. DESeq2 analyzed differential expressions. qPCR validations for samples exposed to amoxapine, ch

Gliomas constitute a heterogeneous group of primary brain cancers, being glioblastoma (GBM) the most prevalent and aggressive form. Despite intensive research, current biomarkers and therapies are still not applied in a personalized manner, and do not prevent recurrency. H3.3 is a non-canonical, replication-independent histone H3 variant which alterations have gain- and loss-of-function effects in pediatric and adult GBM, respectively. The canonical replication-dependent H3.1/H3.2 variants remain largely unexplored in gliomas. We examined these variants in surgical resections of two independen

Substance use disorders (SUD) remain among the most poorly managed health conditions owing to the lack of effective management tools and treatment. Among substances that are used unhealthily, cocaine has the highest genetic heritability (>70%). The advanced mouse resources of the Collaborative Cross and Diversity Outbred (DO) population are a complementary group of mice that allow for a systems genetic analysis of heritable traits. As part of a NIDA Center for Excellence, we have phenotyped 973 DO mice using the cocaine intravenous self-administration (IVSA) paradigm, the gold standard para

High-fat diet (HFD) and obesity are associated with cognitive dysfunction, depression, and increased anxiety, impacting emotional and social behavior. Additionally, HFD affects the immune system, leading to low-level chronic inflammation involving microglia, the brain’s resident immune cells. Inhibiting microglia alters social behavior, and improves HFD-induced metabolic effects. Hence, this raises the question of whether microglial cells mediate HFD-dependent changes in behavioral outcomes.To investigate the effect of HFD-driven microglial activation on neuronal function, HFD adult CX3CR1GFP/

Tuberous sclerosis complex (TSC) is a genetic disorder caused by mutations in TSC1/2 genes, leading to mTOR pathway dysregulation and diverse cellular impacts. Individuals with TSC face severely heightened risk of autism spectrum disorder (ASD), highlighting a genetic link between the two conditions. To model ASD etiology in the context of TSC, we developed a new mouse model with Tsc2 knockout induced mid-gestation in all postmitotic, GABAergic neurons. As ASD and TSC both involve somatosensory processing challenges, we utilized our mouse model to assess how the mutation affects the cortical a

SMC3 is a major component of the cohesin complex that regulates higher-order chromatin organization and gene expression. Human genetic studies reveal de novo mutations in SMC3 gene, found in patients with Cornelia de Lange syndrome (CdLs). This syndrome is characterized by intellectual disabilities, and behavioral patterns such as self-injury, and metabolic dysregulation. Nonetheless, little is known about the exact role of SMC3 in neuronal maintenance and gene expression especially in adulthood. This study aimed to determine the role of SMC3 in adulthood brain, using in-vivo models of adultho

Astrocytes, with their intricate morphology, pose challenges for cell-specific RNA isolation using traditional methods, which often result in loss of RNA localised in distal processes. We tackle this issue by adopting the RiboTag method (Sanz et al 2009) in RPL22tm1.1Psam mice. This technique isolates ribosome-associated mRNA (translatome) cell-specifically from crude tissue lysates through ribosomal HA tagging via cell-type specific Cre expression. Despite the widespread use of RiboTag, its detailed adaptation for complex cells like astrocytes, especially in high-throughput scenarios, remains

Sleep deprivation represents a significant public health problem in countries around the world, resulting in significant impairments in memory and performance. The hippocampus is particularly susceptible to the effects of sleep deprivation. Increasingly, studies suggest sex-specific behavioral differences occur following acute sleep deprivation, but almost all molecular studies have examined changes in males. Consequently, we investigated changes in gene expression following acute sleep deprivation in female mice at different estrous stages. Following one week of individual housing and pre-han

…We performed RNA-seq to investigate the experience-