Tissue Isolation of the Region Around Locus Coeruleus for Single Nucleus RNA Profiling
By onIsolating tissue from the peri-locus coeruleus region in mice for single nucleus RNA
Iso-Seq mapping to L1HS/PA2 consensus sequence
By onThe protocol describes the steps to map HiFi reads to a consensus sequence and retrieve density plots.
Bulk RNA sequencing analysis
By onThis protocol describes the steps for the bioinformatical analysis of bulk RNA sequencing with a focus on evolutionary young L1s.
Nuclear Isolation of Post-Mortem Brain Tissue for snRNAseq
By onThis protocol details how to isolate nuclei from frozen brain tissue for single nuclear RNA sequencing using 10x Genomics GEM isolation using the Chromium accessory and Single Cell 3ʹ Reagent Kits.
Protocols for “Characterizing the diversity of enteric neurons using Dopamine Transporter (DAT)-Cre reporter mice”.
By onThis is a collection of protocols associated to the manuscript "Characterizing the diversity of enteric neurons using Dopamine Transporter (DAT)-Cre reporter mice".
mRNA purification by translating ribosome affinity purification (TRAP) of DAT-expressing cells (dopaminergic neurons) in mouse ventral midbrain
By onThis protocol describes the capture of eGFP-L10a-tagged ribosomes and mRNA from DAT-expressing cells (dopaminergic neurons) in mouse ventral midbrain.
Section 3: Libraries quality control (QC)
By onThis protocol details quality control of libraries and should be performed after Section 2: NGS library preparation for sequencing.
Fluorescence-activated nuclei sorting (FANS) for single-cell Whole Genome Sequencing (scWGS)
By onProtocol for isolating nuclei from human brain samples for low coverage scWGS to detect CNVs. Can be adapted for different body areas, cell cultures, and species.
Nuclei isolation, immunostaining, and Fluorescence-activated nuclei sorting (FANS) for Smart-Seq2
By onThis protocol outlines extracting nuclei from postmortem human brain samples, immunofluorescence, and nuclei sorting for single-nucleus RNA-seq using Smart-Seq2. Applicable to various body areas, cell cultures, and species.
Nova-ST Chip Preparation Protocol
By onNova-ST is a high-resolution spatial transcriptomics workflow using nano-patterned Illumina NovaSeq 6000 S4 flow cells. It offers customizable, cost-effective profiling of tissue sections.
Nova-ST Spatial Transcriptomics protocol
By onNova-ST is an open-source spatial transcriptomics workflow using high-resolution sequencing, comparable to other methods. It enables flexible and low-cost profiling of tissue sections up to 10mm x 8mm.
Oxford Nanopore Technologies (ONT) library preparation and sequencing of DNA prepared using droplet Multiple Displacement Amplification (dMDA)
By onDebranching of DNA generated by Multiple Displacement Amplification (MDA) is an essential step prior to nanopore sequencing. This protocol describes an optimized debranching protocol for genomic DNA amplified from single nuclei using droplet MDA
SureSelect XT HS2 DNA to prepare libraries for single-cell Whole Genome Sequencing (scWGS) after single-cell Whole Genome Amplification (scWGA)
By onSureSelect XT HS2 DNA protocol was modified for library prep for Illumina scWGS using scWGA samples. Protocol can be done manually or with Bravo Automated Liquid Handling Platform for automation.
Sequencing dMDA Products on the MinION using Oxford Nanopore’s Rapid Barcoding Kit
By onLong read sequencing is done on single nuclei dMDA products using MinION & Rapid Barcoding kit. Through this protocol, we can produce and sequence libraries generated from dMDA products.
Human Postmortem-Derived Brain Sequencing Collection (Harmonized Collection)
By onThe Human Postmortem-derived Brain Sequencing Collection is a harmonized repository comprised of sequencing data contributed by ASAP CRN teams.
Protocol for quantitative bulk transcriptomics of striatal tissue
By onProtocol used in the Mazmanian lab for quantitative bulk transcriptomics of mouse striatum tissue
