BrainPalmSeq: A curated RNA-seq database of palmitoylating and de-palmitoylating enzyme expression in the mouse braindoi:10.1101/2021.11.23.468539Angela R WildPeter HoggStephane FlibotteShernaz BamjiCold Spring Harbor Laboratory
t-SNE visualization of region-specific genes on TCGA tumor data. t-SNE was performed using TCGA RNAseq data from brain region sub-GCN genes. 1431 tumor samples from four tumor subtypes are shown. Tumor RNA expression profiles sorted regions into multiple clusters. Each color represents different...
To tackle brain oGPCR anatomy in the brain, we fine-map their expression in the mouse brain using dedicated probes in two complementary in situ hybridization (ISH) approaches, and create a database of all images, posted as an open-access resource athttp://ogpcr-neuromap.douglas.qc.ca. Fu...
facilitating the analysis of a group of genes. For the adult and developing human atlases, the gene expression data (microarray or RNA-seq) are mainly visualized using heatmaps (Fig.2d). In the adult human atlas, the expression data can also ...
(AMS), which is difficult to diagnose due to the lack of effective molecular markers. AMS is a type of hypoxic ischemic necrosis with no more than four points on the NIHSS. Recently, many lncRNAs associated with AMS have been gradually discovered. Using RNA-seq, lncRNAs were identified in ...
Cluster 13 cells expressing the interferon-related module were roughly twice as abundant in 5XFAD brains (0.9%) than in controls (0.4%), and we also observed a similar ∼doubling of this population using single-cell RNA-seq in the PS2APP model (unpublished data). Our gene sets therefore ...
STAR: ultrafast universal RNA-seq aligner Bioinformatics, 29 (2013), pp. 15-21 Google Scholar Edgar et al., 2002 R. Edgar, M. Domrachev, A.E. Lash Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res., 30 (2002), pp. 207-210 Google ...
Fully formatted Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts ...
ROSMAP and Mount Sinai RNA batch correction and pre-processing Regression of the RNA-seq data was modeled on Sieberts et al.58,59. Raw RNA counts were loaded, and variance partitioning was determined. Genes that were expressed at a level of more than 1 count per million (CPM) total reads...
In order to better understand the relationship between normal and neoplastic brain, we combined five publicly available large-scale datasets, correcting for batch effects and applying Uniform Manifold Approximation and Projection (UMAP) to RNA-Seq data. We assembled a reference Brain-UMAP including 702...