Project description:Mouse brain 10x Genomics Visium Spatial Transcriptomics profiles sequence either with Illumina for standard profiling and Nanopore promethION long read sequencer for full-length profiling.
Project description:E18 mouse brain single cell profiling using the 10x Genomics Chromium instrument workflow with either Illumina short read sequencing for the standard gene profiling and Nanopore PromethION long read sequencing for isoform profiling.
Project description:Oxford Nanopore enables direct RNA sequencing allowing for base calling of RNA modifications. We tested mouse hippocampi RNA samples, using a Nanopore direct RNA-seq protocol that in addition to long poly A selected RNAs allows sequencing also of non-poly A RNAs as well as short RNAs < 200nt (including SINE B2 RNAs and other non poly A non coding RNAs). We provide here as a resource a direct RNA-sequencing dataset generated from mouse brain tissues that includes both mRNAs and non poly A or short non-coding RNAs such as SINEs. Elevated SINE B2 RNA Adenosine to Inosine editing is consistently observed across hippocampal tissues of a mouse model of amyloid beta accumulation compared to hippocampi of wild type animals. Nanopore direct RNA sequencing supports increased RNA modification signals at the sameSINE B2 RNA regions identified by short-read Illumina sequencing in these hippocampi.
Project description:Affymetrix OncoScan data from primary and metastatic intracranial lesions collected for the validation of our intraoperative brain tumor classification with nanopore sequencing. All samples were processed from FFPE by our clinical lab using the standard protocol for clinical samples.
Project description:iCLIP experiments tomap the RNA binding sites of the RNA-binding protein Unkempt across the transcriptome in SH-SY5Y cells, HeLa cells with ectopic Unk expression and mouse E15 embryonic brain samples. Expression of Unk is normally largely restricted to the nervous system. We therefore mapped the binding sites in human SH-SY5Y and mouse E15 brain to detect its physiological binding sites (in SH-SY5Y, we also performed the RNAseq experiment upon Unk knockdown). HeLa cells on the other hand normally don't express Unk, but convert to neuron-like shape when the protein is ectopically expressed. So, here we hoped to identify those binding events (and hence target transcripts) that are critical for this morphological transformation.
Project description:We create catalogues of genes showing significant strain, parent-of-origin, dominance, sex effect in inbreds and reciprocal F1 hybrids of three wild-derived strains (CAST, PWK, WSB) across 4 different tissues (brain, kidney, liver, and lung) We used microarrays to validate the Brain results of RNAseq from inbred and F1 of 3 by 3 diallel. Brain, liver, kidney and lung RNA from the same mice used for RNAseq were hybridized to Affymetrix Mouse Gene 1.1 ST 96-Array Plate arrays using a GeneTitan instrument from Affymetrix.