Apr 29, 2026
Bulk RNA Extraction from Mouse Striatum
- Sriparna Mukherjee1,2,3,4,
- Louis-Éric Trudeau1,5,2,3,6,4
- 1Department of pharmacology and physiology, Faculty of Medicine, Université de Montréal;
- 2Neural Signaling and Circuitry research group (SNC);
- 3Center for Interdisciplinary Research on the Brain and Learning (CIRCA);
- 4Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815;
- 5Department of neuroscience and physiology, Faculty of Medicine, Université de Montréal;
- 6Institut Courtois d’innovation biomédicale
Protocol Citation: Sriparna Mukherjee, Louis-Éric Trudeau 2026. Bulk RNA Extraction from Mouse Striatum. protocols.io https://dx.doi.org/10.17504/protocols.io.14egn5qrqg5d/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 21, 2026
Last Modified: April 29, 2026
Protocol Integer ID: 315475
Keywords: bulk rna extraction from mouse striatum, bulk rna extraction, downstream bulk rna, isolation of total rna, dissected mouse striatal tissue, total rna, mouse striatum, rna integrity, striatal tissue, qiagen rneasy mini kit, sequencing analysis, dissected mouse, montreal genomics platform
Funders Acknowledgements:
Aligning Science Across Parkinson's
Grant ID: ASAP-000525
Abstract
This protocol describes the isolation of total RNA from dissected mouse striatal tissue using the Qiagen RNeasy Mini Kit (Cat. No. 74104) for downstream bulk RNA sequencing analysis. RNA integrity and quality were assessed using an Agilent BioAnalyzer. For each sample, 600 ng of total RNA was used for library preparation and subsequent sequencing at the University of Montreal Genomics Platform.
Guidelines
Work in an RNase-free environment throughout the procedure. Always wear gloves. Use only RNase-free tubes, filtered tips, and reagents. Keep tissue frozen until lysis and minimize sample thawing time. Neural tissue is prone to rapid RNA degradation, so efficient processing is important for obtaining high-integrity RNA suitable for sequencing.
Quality check in Nanodrop:
For RNA, the commonly accepted purity ranges are:
260/280: about 1.9 to 2.1. This reflects low protein contamination. For high-quality RNA, values close to 2.0 are generally expected.
260/230: about 2.0 to 2.2. Lower values can suggest contamination from salts, phenol, guanidine, or other extraction carryover.
These ratios are useful, but RNA integrity matters as well. A good RIN or BioAnalyzer trace is often more important than a perfectly ideal Nanodrop ratio.
Materials
- Mouse striatal tissue
- RNeasy Mini Kit (Qiagen, Cat. no. 74104)
- Trizol
- 70% ethanol, RNase-free or molecular biology grade
- RNase-free water
- RNase-free microcentrifuge tubes
- Homogenizer
- Microcentrifuge
- Pipettes with RNase-free filtered tips
- Ice bucket
- Nanodrop
Safety warnings
This procedure uses lysis reagents that may be harmful if inhaled or brought into contact with skin or eyes. Follow institutional safety procedures and consult the reagent safety data sheets before use. Wear a lab coat and gloves as needed. Dispose of tissue waste and chemical waste according to institutional biosafety regulations.
Before start
Prepare all kit reagents according to the manufacturer’s instructions, including addition of ethanol to wash buffers as required by the kit. Pre-clean the work surface and tools with an RNase decontamination agent. Label all tubes before beginning.
Tissue collection and storage
Dissect the striatum from the mouse brain using clean instruments.
Immediately place each sample into a pre-labeled RNase-free microcentrifuge tube.
Either proceed directly to extraction or snap freeze tissue and store at -80 °C until use.
Tissue lysis and homogenization
Add the appropriate volume of Trizol to the striatal tissue.
(300 µL of Trizol is used for the entire striatum isolated from both hemispheres of the brain)
Homogenize the tissue thoroughly until the lysate is uniform and no visible fragments remain.
Critical step: Incomplete homogenization can reduce yield and clog the column. Brain tissue should be fully disrupted before proceeding.
Preparation for RNA binding
Add equal volume of 70% ethanol to the homogenized lysate.
Mix well by pipetting or gentle inversion until the solution is homogeneous.
Binding RNA to the silica membrane
Transfer the sample to a RNeasy spin column placed in a collection tube.
(700 µL at a time)
Centrifuge according to the kit's instructions to allow binding of the RNA to the membrane.
Discard the flow-through.
If the full lysate volume exceeds the column capacity, reload the remaining lysate and repeat until all material has passed through the column.
Column washing
Wash the column using the kit-provided wash buffers (RW1 and RPE) in the sequence and volume specified by the supplier.
Centrifuge after each wash step as directed by the manufacturer.
Perform the final dry spin to remove residual wash buffer and ethanol.
Critical step: Residual ethanol can interfere with downstream RNA quantification, quality assessment, enzymatic reactions, and library preparation.
RNA elution
5m
Transfer the spin column to a clean RNase-free microcentrifuge tube.
Add RNase-free water (30 µL ) directly onto the membrane.
Incubate for 00:05:00 .
5m
Centrifuge to elute RNA.
Critical point: Purified RNA may be stored temporarily on ice for immediate quality measurements or at -80°C for long-term storage.
Quality control and downstream application
Measure RNA concentration using a Nanodrop.
Assess RNA quality and integrity using an Agilent BioAnalyzer or other similar instrument.
RNA with a good RIN (RNA integrity number) can be used for RNA sequencing.
Data collection in Tabular Form
Data collection in Tabular Form (example)