Instructions & Guidelines

Ordering via NUCORE

Sample Submission Instructions

Multi-Organ Submission Policy

A "multi-organ submission" refers to multiple tissue types and organs derived from a single experimental animal. Please read our MULTI-ORGAN SUBMISSION POLICY.

ISH/RNAscope Order Guidelines

MHPL Guidelines for In Situ Hybridization (ISH) and RNAscope Services

Intercampus Courier Label

Intercampus Courier Shipping Label

VALIDATING ORDER NUMBERS

Download step-by-step instructions to validate your order at NUCORE.

MHPL Service Rates

Download here the pricing for our services:

MHPL SERVICE RATES FY25

Staging Mouse Embryos

Mouse embryos can be staged according to a variety of criteria, the most general of which are those described by Theiler in "The House Mouse: Atlas of Mouse Development" (Springer-Verlag, New York, 1989).

Theiler Criteria for Staging Mouse Embryos

Atlas of Mouse Development

The following eHistology online resource provides free access to high-resolution colour images digitized from the original histological sections used by Kaufman for the Atlas of Mouse Development (1994).

eMouseAtlas 

Histology Atlas of the Mouse Placenta

The following paper provides an overview of histological transformations during the development of the mouse placenta which can be useful in identifying and describing changes in engineered, induced, and spontaneous disease models.

HISTOLOGY ATLAS OF MOUSE PLACENTAL DEVELOPMENT

Histology Atlas of Mouse Urinary System Development

This review focuses on the histology of the mouse urinary system during embryonic development.

ATLAS OF MOUSE EMBRYONIC DEVELOPMENT OF THE URINARY SYSTEM

Histology Atlas of Mouse Heart Development

Histology of Mouse Lung Development

Histology Atlas of Liver Development

Brain Atlases

The ALLEN BRAIN MAP is an excellent resource in neuroscience research and includes neuroanatomical atlases for mouse CNS, and human brain across multiple developmental timepoints.

Anatomy & Histology of the Pancreas

Non-Neoplastic Lesion Atlas

The Non-Neoplastic Lesion Atlas hosted by the National Toxicology Program is a guide for standardizing toxicologic pathology in rodents. The atlas is subdivided into chapters covering a single organ. 

Sampling of Rodent Organs for Histology

The following papers summarize suggested guidelines for preparing various organs in tissues from rodents for histological analysis.

Tissue Collection for Systematic Mouse Phenotyping

Respiratory, Reproductive and Thymic Organs

Neuronal, Urogenital Tract, Cardiovascular, and Immune Organs

Intestinal Swiss Rolls

Fixation of Lungs for Histology

Tracheal Perfusion with Fixative

Lung Air-Inflation Vascular Perfusion-Fixation

Transcardial Perfusion-Fixation

This method is the preferred fixation strategy for CNS tissues and also to flush out blood from organs.

Intracardiac Perfusion-Fixation

Glyoxal Fixation

Glyoxal can replace formaldehyde-based fixatives (10% NBF or 4% PFA) as a fast-acting cross-linker that also preserves protein and nucleic acid antigenicity. Glyoxal-fixation typically results in brighter microscopy images.

Glyoxal Fixation Protocol

Lipid Fixation with Chromic Acid

Chromic acid can fix lipids in tissues prior to creation of FFPE blocks. This is a convenient alternative to cryosections for evaluation of lipid accumulation. 

Chromic Acid Fixation of Lipids for FFPE

Fixation of Ocular & Testicular Specimens

Davidson's Fixative for Eyes and Testes

Recipe for Modified Davidson's Fixative

Heart Tissue Processing for Infarct Analysis

This protocol describes the use of a tissue matrix to sample thick sections of the heart for a systematic survey of myocardial infarct.

Histological Analysis of Myocardial Infarct

Decalcification with Immunocal

This method is a formic acid-method using IMMUNOCAL for decalcifying mineralized tissues to make them suitable for microtomy and subsequent histology and immunostainings.

Decalcification with EDTA

This method for decalcification utilizes a buffered EDTA-sucrose solution. This method is suitable for spatial transcriptomics to maintain the integrity of RNA in the tissues.

Cryostat Self-Service

Leica CM1850UV User Manual

OCT Embedding

Simultaneous freezing and embedding of fresh tissue in OCT for cryosectioning.

Dakewe CT520 Cryostat User Manual

Cryosectioning Tutorial

Vibratome Self-Service Policies

Leica VT1200S User Manual

Vibratome Sectioning of Rodent Brain Slices

Mouse Brain Sectioning with the Vibratome

Rat Brain Sectioning with the Vibratome

Sectioning of Thick Liver Slices

Optimization of Vibratome Sectioning

Histogel Embedding

Alginate Embedding

Prepare Slides of Single Cell Suspensions

The Cytospin method prepares single cell suspension smears on glass slides by centrifugation suitable for downstream histology, immunostaining, or nucleic acid in situ hybridization.

Selection of Antibodies

CITEAB is a useful website summarizing applications and published citations for commercially available antibodies.

Selecting Positive Control Tissues

Here are useful resources for identifying positive control tissues for immunolabelings and in situ hybridization:

NCBI GENE

HUMAN PROTEIN ATLAS

CELL MARKER

Fiji / ImageJ

FIJI/ImageJ is a widely used, free, and open-source software platform for scientific image analysis.

QuPATH

QuPATH is an open-source, cross-platform software application primarily used for bioimage analysis, particularly within the context of digital pathology and whole slide image analysis.

CellProfiler

CellProfiler is a free, open-source image analysis software designed for biologists to automatically identify, quantify, and analyze biological entities in images. It allows users to create custom pipelines using various image processing and object analysis modules, facilitating reproducible and quantitative analysis of cell and subcellular features.

RNAscope Data Analysis

This ACD web resource  provides a wealth of information on how to analyze RNAscope data in chromogenic singleplex/duplex to multiplex fluorescent scenarios.

CellProfiler Analysis of RNAscope & BASEscope Data

This ACD web resource provides instructions on how to analyze RNAscope or BASEscope results using CellProfiler.

3D Printing Brain Matrices

This protocol provides instructions on how to 3D print mouse brain slicing matrices.

Custom Mouse Brain Matrix

3D Printing Services are available at:

MakerLab at the Mudd Library in the Evanston campus.

CAM/NIC at Searle Bldg. in the Chicago campus.

3D Printing of Tissue Sectioning Matrix

3D Printing Tissue Matrix

Tissue Matrix 3D Printing Template 

3D Printing Services are available at:

MakerLab at the Mudd Library in the Evanston campus.

CAM/NIC at Searle Bldg. in the Chicago campus.

Thick Slicing of Brain & Heart Using a Tissue Matrix

This instructional video shows how to systematically slice thick sections of brain and heart tissues using a tissue matrix.