Methods to Enable Spatial Transcriptomics of Bone Tissues

Luigi Mancinelli; Karen Elizabeth Schoedel; Kurt Richard Weiss; Giuseppe Intini

doi:10.3791/66850

JoVE Journal > Developmental Biology

Biologia dello sviluppo

Methods to Enable Spatial Transcriptomics of Bone Tissues

Published: May 03, 2024

doi:

10.3791/66850

Luigi Mancinelli^1,2, Karen Elizabeth Schoedel^3,4, Kurt Richard Weiss^5,6,7, Giuseppe Intini^1,2,8,9,10

¹Department of Periodontics and Preventive Dentistry,University of Pittsburgh School of Dental Medicine, ²Center for Craniofacial Regeneration,University of Pittsburgh School of Dental Medicine, ³UPMC Presbyterian, ⁴UPMC Shadyside, ⁵Musculoskeletal Oncology Laboratory, Department of Orthopaedic Surgery,University of Pittsburgh, ⁶UPMC Hillman Cancer Center, ⁷Departments of Anatomic Pathology and General Surgical Oncology,University of Pittsburgh, ⁸Department of Medicine,University of Pittsburgh School of Medicine, ⁹University of Pittsburgh UPMC Hillman Cancer Center, ¹⁰McGowan Institute for Regenerative Medicine,University of Pittsburgh

Summary

Here, we describe a method that allows for the decalcification of freshly obtained bone tissues and the preservation of high-quality RNA. A method is also illustrated for sectioning Formalin Fixed Paraffin Embedded (FFPE) samples of non-demineralized bones to obtain good quality results if fresh tissues are not available or cannot be collected.

Abstract

Understanding the relationship between the cells and their location within each tissue is critical to uncover the biological processes associated with normal development and disease pathology. Spatial transcriptomics is a powerful method that enables the analysis of the whole transcriptome within tissue samples, thus providing information about the cellular gene expression and the histological context in which the cells reside. While this method has been extensively utilized for many soft tissues, its application for the analyses of hard tissues such as bone has been challenging. The major challenge resides in the inability to preserve good quality RNA and tissue morphology while processing the hard tissue samples for sectioning. Therefore, a method is described here to process freshly obtained bone tissue samples to effectively generate spatial transcriptomics data. The method allows for the decalcification of the samples, granting successful tissue sections with preserved morphological details while avoiding RNA degradation. In addition, detailed guidelines are provided for samples that were previously paraffin-embedded, without demineralization, such as samples collected from tissue banks. Using these guidelines, high-quality spatial transcriptomics data generated from tissue bank samples of primary tumor and lung metastasis of bone osteosarcoma are shown.

Introduction

Bone is a specialized connective tissue comprised mainly of fibers of collagen type 1 and inorganic salts¹. As a result, bone is incredibly strong and stiff while being, at the same time, light and trauma-resistant. The great strength of bone derives from its mineral content. In fact, for any given increase in the percentage of mineral content, stiffness increases by five-fold². Consequently, investigators face significant problems when they analyze, by means of histological sectioning, the biology of a bone specimen.

Undecalcified bone histology is feasible and sometimes required, depending on the type of investigation (e.g., to study the micro-architecture of bone); it is, however, very challenging, especially if the specimens are large. In these cases, tissue processing for histological purposes requires several modifications of the standard protocols and techniques³. In general, to perform common histological evaluations, bone tissues are decalcified right after fixation, a process that may require a few days to several weeks, depending on the size of the tissue and the decalcifying agent utilized⁴. Decalcified sections are often used for the examination of bone marrow, the diagnosis of tumors, etc. There are three main types of decalcifying agents: strong acids (e.g., nitric acid, hydrochloric acid), weak acids (e.g., formic acid), and chelating agents (e.g., ethylenediaminetetracetic acid or EDTA)⁵. Strong acids can decalcify bone very rapidly, but they can damage the tissues; weak acids are very common and suitable for diagnostic procedures; chelating agents are by far the most used and appropriate for research application since, in this case, the demineralization process is slow and gentle, allowing for retention of high-quality morphology and preservation of gene and protein information, as required by many procedures (e.g., in situ hybridization, immunostaining). However, when the whole transcriptome needs to be preserved, such as for gene expression analyses, even a slow and gentle demineralization may be detrimental. Therefore, better approaches and methods are needed when the morphological analysis of the tissues needs to be paired with gene expression analyses of the cells.

Thanks to recent improvements in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics, it is now possible to study the gene expression of a tissue specimen even when formalin fixation paraffin embedding (FFPE) was used to store the tissue samples⁶^,⁷^,⁸. This opportunity has unlocked access to a larger number of samples, such as those stored in tissue banks worldwide. If scRNA-seq is to be employed, RNA integrity is the most important requirement; however, in the case of spatial transcriptomics of FFPE samples, both high-quality tissue sections and high-quality RNA are necessary to visualize the gene expression within the histological context of each tissue section. While this has been easily achieved with soft tissues, the same cannot be said for hard tissues like bone. In fact, to the best of our knowledge, no study using spatial transcriptomics has ever been performed on FFPE bone samples. This is because of the lack of protocols that can effectively process FFPE bone tissues while preserving their RNA content. Here, a method to process and decalcify freshly obtained bone tissue samples while avoiding RNA degradation is provided first. Then, recognizing the need for transcriptomics analysis of the FFPE samples collected in tissue banks worldwide, developed guidelines to properly handle FFPE samples of non-demineralized bones are also presented.

Protocol

All animal procedures described below were approved in compliance with the Guide for the Care and Use of Laboratory Animals at the University of Pittsburgh School of Dental Medicine.

1. Method to prepare FFPE blocks of bone tissue samples that require demineralization

Preparation of reagents and materials
1. Prepare EDTA 20% pH 8.0. For 1 L, dissolve 200 g of EDTA in 800 mL of ultrapure water, adjust pH to 8.0 with sodium hydroxide 10 N and finally bring the volume to 1L with ultrapure water. Store at room temperature.
  NOTE: Always use freshly prepared EDTA 20% pH 8.0. Sodium hydroxide (NaOH) 10 N is prepared by dissolving 400 g of NaOH in 1 L of ultrapure water.
2. Prepare paraformaldehyde (PFA) 4% in a fume hood utilizing 1x PBS without calcium and magnesium.
  NOTE: Designate an area in a fume hood for working with concentrated paraformaldehyde solutions, or paraformaldehyde solids, and label it as such. To avoid exposure, keep containers closed as much as possible. Use in the smallest practical quantities needed for the experiment being performed. If weighing paraformaldehyde powder and the weighing scale cannot be used in a fume hood, first take a container, then add PFA powder in the hood and cover before returning to the scale to weigh the powder. Always use freshly prepared 4% PFA.
3. Use a suitable container for each specimen.
  NOTE: For instance, for 1 mg of bone tissue, use a container that allows for at least 1 mL of any solution to be in contact with the bone.
4. Sterilize all the surgical equipment needed for dissection.
5. Clean all the areas with a decontaminating solution to remove RNases.
6. Collect the remaining experimental materials, including ice containers, 70% ethanol spray, and have access to an orbital shaker.
Isolation of bone tissue samples from mice
1. Euthanize the mouse by CO₂ exposure, then perform cervical dislocation and lay it on its back. Spray the mouse skin with 70% ethanol.
2. Using sterile dissecting scissors, open the skin and expose the leg muscle. Cut the muscle alongside the leg to obtain a clear view of the position of the bone, and gently disarticulate the bone to remove it without damage.
  NOTE: It is not necessary to remove entirely all the muscle attached to the bone. Try to be as fast as possible to limit RNA degradation.
3. Immediately place the bone sample in a tube containing 4% PFA and place the tube on ice.
4. Repeat the procedure to collect other bone samples as desired.
5. Put samples with 4% PFA in agitation on an orbital shaker at 140 rpm at 4 °C for at least 24 h to allow proper fixation.
Decalcification of bone tissue samples
1. Retrieve the bone tissue from the orbital shaker after fixation.
2. Wash the bone tissue 2 times with 1x PBS for 3 min on an orbital shaker at 140 rpm to remove any PFA left.
3. Using sterile dissecting scissors, remove any remaining muscles still attached to the bone.
4. Wash the bone tissue one more time with 1x PBS for 3 min.
5. Place the bone tissue in a new container with 20% EDTA pH 8.0. Then, place the container on an orbital shaker at 140 rpm for 30 min at room temperature (RT).
6. Discard the solution, add fresh 20% EDTA pH 8.0 in the container, and place it on an orbital shaker at 140 rpm for 30 min at RT.
7. Repeat step 1.3.6 10 times.
8. Discard the solution, add fresh 20% EDTA pH 8.0 in the container, and place it at 4 °C in a cold room on an orbital shaker at 140 rpm overnight.
Dehydration of bone tissue samples
1. Retrieve the bone tissue sample from the container.
2. Inspect the tissue and verify the efficiency of decalcification by gently turning and twisting the bone. Alternatively, perform an X-ray of the bone using an X-ray machine.
  NOTE: If the specimen flexes easily, a good grade of decalcification has been achieved. If not, decalcification parameters (time, speed of agitation, volume of 20% EDTA pH 8.0. used, etc.) should be increased.
3. Wash the bone tissue 2 times with 1x PBS for 3 min to remove residues of EDTA.
4. Place the bone tissue in a new container and initiate dehydration with 70% ethanol. Incubate for 15 min at 140 rpm.
5. Discard the 70% ethanol solution, put the sample in 90% ethanol solution, and incubate for 15 min at 140 rpm.
6. Discard the 90% ethanol solution, put the sample in 100% ethanol, and incubate for 15 min at 140 rpm.
7. Discard the 100% ethanol, put the sample in new 100% ethanol, and incubate for 15 min at 140 rpm.
8. Discard the 100% ethanol, put the sample in new 100% ethanol, and incubate for 15 min at 140 rpm.
9. Discard the 100% ethanol, put the sample in new 100% ethanol, and incubate for 30 min at 140 rpm.
10. Discard the 100% ethanol, put the sample in new 100% ethanol, and incubate for 45 min at 140 rpm.
  NOTE: Dehydration can also be performed using an automatic processor. In this case, set up the program with the same conditions reported for the manual dehydration. The reported conditions are for specimens no thicker than 4 mm (i.e., bone tissue samples obtained from mice). For specimens thicker than 4 mm, dehydration timing must be determined experimentally.
Clearing of bone tissue samples
1. Place the bone tissue sample in a new container and initiate the clearing process using xylene. Incubate for 20 min at 140 rpm.
2. Discard the used xylene, add new xylene, and incubate for an additional 20 min at 140 rpm.
3. Discard the used xylene, add new xylene, and incubate for 45 min at 140 rpm.
  NOTE: Clearing can also be performed using an automatic processor. In this case, set up the program with the same conditions reported for the manual clearing. The reported conditions are for specimens no thicker than 4 mm (i.e., bone tissue samples obtained from mice). For specimens thicker than 4 mm, the timing must be determined experimentally.
Infiltration and embedding of bone tissue samples
1. Retrieve the bone tissue sample from the orbital shaker/automatic processor after clearing.
2. Place the bone tissue sample in an embedding cassette and initiate infiltration with wax (see Table of Materials). Incubate for 30 min at 60 °C.
3. Discard the used wax, add new wax, and incubate for 30 min at 60 °C.
4. Discard the used wax, add new wax, and incubate for 45 min at 60 °C.
5. Carefully place the bone tissue sample in a mold with the desired orientation.
6. Allow the specimen block to solidify on a cold surface.
7. Store the obtained FFPE at 4 °C until ready to start sectioning.
  NOTE: FFPE block can be stored for many years before sectioning is carried out.

2. Guidelines for sectioning un-demineralized FFPE samples

NOTE: The following guidelines provide valuable tips and instructions useful to greatly improve the quality of the tissue sections while avoiding RNA degradation especially in cases of small undecalcified bone specimens. These guidelines may also be applied to decalcified bone specimens when available. For larger bone tissue samples, demineralization should be performed to obtain better quality sections; in such cases, the method reported above should be followed, and parameters (timing, volumes of solutions, etc.) should be adjusted accordingly. The following guidelines are suitable either when FFPE bone tissues have already been processed (e.g., FFPE block collected from tissue banks or other labs) or when the collected sections will be utilized to perform any type of analysis that requires good quality RNA, high-quality tissue sections, or both.

Equipment preparation
1. Spray all work surfaces and instruments with decontaminating solutions to remove RNases.
2. Prepare a water bath with double distilled water and set the temperature to 42 °C.
3. Take a microtome blade, spray it with 70% ethanol to remove oil residues, then spray it with decontaminating solutions to remove RNases.
4. Secure the blade on the microtome. Ensure that the clearance angle is set to 10°.
  NOTE: Always use new blades for sectioning.
5. Prepare two buckets of ice.
6. Get tweezers, brushes, and probes, spray them with decontaminating solutions to remove RNases, and place them in one of the two ice buckets.
7. Prepare an ice bath by adding double distilled water to the other ice bucket.
  NOTE: the FFPE block should not float in the added water; therefore, the amount of added water to the ice bucket must be just enough to allow the sample to be wet without floating.
Sectioning
1. Retrieve the FFPE block from storage at 4 °C and place it on the microtome. Set the command to Trim or to 14 µm of scroll thickness, and start trimming the sample until the tissue is exposed.
  NOTE: If the FFPE block has already been trimmed and the tissue is already exposed, skip step 2.2.1. Verify that the block is without holes and cracks. If so, proceed directly to step 2.2.2. If not, cut a few sections to flatten the surface and avoid the holes and cracks, and then proceed to step 2.2.2.
2. Place the FFPE block on the ice bath to hydrate the sample. The time of hydration must be determined experimentally.
  1. Start with 2 min and increase the time if hydration is not enough. Do not exceed 10 min. The hydration will expand the tissue and reduce the formation of "Venetian blinds" and lines. Longer hydration times could cause cracks in the paraffin block and, possibly, tissue detachment.
  2. If 10 min is insufficient to hydrate the sample, then perform hydration cycles no longer than 10 min and attempt sectioning again.
  3. If the surface of the block is not smooth and clean due to cracks or cuts, consider re-embedding the sample. RNA quality will not be affected by the re-embedding process.
3. Put the sample in the specimen clamp of the microtome, align it with the blade, and start sectioning. Set the scroll thickness to 5 µm.
4. Collect the section and place it in the water bath at 42 °C using cold tweezers and brushes.
  NOTE: Alternatively, if RNA isolation of tissue sections will be performed, collect the sections in a centrifuge tube and follow the manufacturing specifications for RNA preparation (see Table of Materials).
5. Incubate the section in the water bath to stretch the tissue and eliminate any residual wrinkles and folds.
  NOTE: The time of floating in the water bath for each section must be determined experimentally. Consider leaving the bone sections an extra minute if tissue detachment issues occur. Do not leave the section floating too long since long floating times could damage the tissue.
6. Place the section on a glass slide, then incubate it for 3 h at 42 °C.
7. Place the glass slide in a desiccator or an oven overnight at RT for proper drying.
8. Store the glass slide with the attached section at RT in a slide box.
  NOTE: Slides can be stored for many years at RT. If spatial transcriptomic will be performed, instead of a glass slide, place the section on the spatial gene expression slide provided by the manufacturer and follow the reported recommendations (see the Table of Materials).

Representative Results

The method presented here describes how to process freshly isolated bones to obtain demineralized FFPE samples that can be easily sectioned with a microtome while preserving the RNA integrity (Figure 1). The method has been successfully employed on murine femurs but can be followed for other bone tissue samples of similar dimensions, or it can be adapted for larger bone specimens (e.g., human samples) by increasing all the parameters (timing, volumes of solutions, etc.).

Figure 1: Schematic representation of the protocol. Schematic diagram of the method to obtain FFPE blocks of decalcified bone tissues with preserved RNA integrity (points 1 and 2). Schematic diagram of the guidelines to section FFPE blocks (point 3). Please click here to view a larger version of this figure.

To validate the correct timing of decalcification, a time course was performed in which undecalcified femurs, femurs decalcified for 3 h (for which EDTA was changed every 30 min for a total of 6 times), and femurs decalcified for 24 h (for which EDTA was changed every 30 min for a total of 10 times and then left in EDTA overnight) were compared (Figure 2). The obtained FFPE blocks were then sectioned according to the above guidelines, and the histological quality and RNA integrity of the obtained sections were verified. To do so, the structural integrity and the morphology of tissue sections were evaluated by means of hematoxylin and eosin (H&E) staining followed by microscopic inspection (Figure 2A,C,E), while the RNA quality was assessed by evaluating the RNA fragment distribution value with size higher than 200 nucleotides (200 nt)(known as DV200 score)⁴ (Figure 2B,D,F). H&E images showed that undecalcified and 3 h decalcified femur sections presented with several fractures, holes, and damages (Figure 2A,C,), while sections of femurs decalcified for 24 h displayed good histological quality (Figure 2E). All the samples presented DV200 scores higher than 50%, which is considered the minimum value to perform scRNA-seq or spatial transcriptomic analyses⁴. Longer incubation times with daily changes of EDTA, at 4 °C, with milder agitation in smaller containers, were also tested and are not recommended since, using these conditions, the RNA integrity of the samples declines dramatically (Figure 2H). Therefore, the time of incubation was decreased to 24 h while the frequency, agitation, and volumes of decalcification were increased to boost decalcification.

Figure 2. Sections and RNA integrity quality control (QC) of 8-week-old mouse femurs after decalcification. Femurs from 8-week mice were freshly dissected, fixed, and decalcified with 20% EDTA pH 8.0. at different time points, embedded in paraffin using the described method, and sectioned following the reported guidelines. Histological QC of obtained sections was then performed by means of H&E staining, while RNA integrity was assessed by evaluating the RNA Fragment Distribution Value with a size larger than 200 nucleotides (200 nt)(DV200). (A) H&E staining showing 8 week-old mouse femur sections after no decalcification. The right image shows a higher magnification of the boxed area. (B) RNA QC of 8 week-old mouse femur sections after no decalcification. (C) H&E staining showing 8 week-old mouse femur sections after 3 h of decalcification. The right image shows a higher magnification of the boxed area. (D) RNA QC of 8 week-old mouse femur sections after 3 h of decalcification. (E) H&E staining showing 8 week-old mouse femur sections after 24 h of decalcification. The right image shows a higher magnification of the boxed area. (F) RNA QC of 8 week-old mouse femur sections after 24 h of decalcification. (G) H&E staining showing 8 weeks-old mouse femur sections after 72 h of decalcification. The right image shows a higher magnification of the boxed area. (H) RNA QC of 8 week-old mouse femur sections after 72 h of decalcification. Abbreviations: H&E = hematoxylin and eosin; DV200 (%) = % of fragment distribution value > 200 nt; nt = nucleotides. Please click here to view a larger version of this figure.

To test the efficacy of the reported guidelines to handle non-demineralized FFPE samples, FFPE blocks of non-demineralized human primary osteosarcoma and lung osteosarcoma metastases obtained from our Musculoskeletal Oncology Tumor Registry and Tissue Bank (MOTOR) were collected, and spatial transcriptomic analysis was performed (Figure 3). Before proceeding with spatial transcriptomic analysis, FFPE blocks were re-embedded in paraffin to obtain a smooth starting surface. Then, the RNA and histological quality of the sections were evaluated (data not shown). Hydration steps were decisive since primary osteosarcoma specimens could not be sectioned without proper hydration. By contrast, lung metastases did not require any hydration steps. After sectioning, tissues were placed on a spatial transcriptomic slide (Figure 3A), stained with H&E (Figure 3D), and spatial transcriptomic analysis was performed according to manufacturer specifications (see Table of Materials). Obtained cDNA libraries were sequenced, and processed data were visualized with Space Ranger for quality control⁵ (Figure 3B). Space Ranger output showed very high scores (nearly 100%) for valid barcodes, valid unique molecular identifiers (UMIs), Q30 bases, and median of detected genes per spot (between 1700 and 5000), demonstrating robustness and solidity of the obtained data (Figure 3B). By means of unbiased graph-based cluster analysis, 12 major clusters were identified, including clusters of osteogenic, immune, epithelial, and endothelial cells, as well as adipocytes (Figure 3E). Of note, the boundaries of the clusters overlapped with the edges of the histological regions identified by the pathologist (Figure 3D). Additional sections of the same samples were also stained with Goldner's Trichrome to visualize mineralized areas (Figure 3C).

Figure 3. Spatial transcriptomic analysis of two pairs of undecalcified primary osteosarcoma (OS) and lung metastases. FFPE blocks of two matching pairs of non-demineralized human primary osteosarcoma and lung metastasis were collected from our MOTOR tissue bank. Samples were sectioned using the reported guidelines and were placed onto a Visium Spatial Gene Expression slide for FFPE samples to perform spatial transcriptomic analysis. (A) Visium Spatial Gene Expression slide for FFPE samples with the attached sections. (B) Space Ranger output showing common parameters used to assess the quality of the obtained data for all samples. (C) Goldner's Trichrome stain showing localization of mineralized bone tissues and osteoid. (D) H&E stain showing the pathologist's annotation. (E) Cluster analysis showing localization of the tissue residing cell populations. Abbreviations: FFPE = formalin-fixed and paraffin-embedded; MOCs = malignant osteogenic cells. Please click here to view a larger version of this figure.

Discussion

Here, a detailed method is provided to prepare FFPE blocks of decalcified bones and preserve RNA integrity for sequencing (i.e., next-generation sequencing (NGS)) or for other RNA-related techniques (i.e., in situ hybridization, quantitative reverse transcription polymerase chain reaction (qRT-PCR), etc.).

The method utilizes EDTA to decalcify bone tissue samples; the EDTA incubation allows for slow but fine demineralization of the samples, thus preserving the histological features of the tissue at their best. Usually, bone decalcification is performed using 10% EDTA pH 7.0 for at least 2 weeks by refreshing the solution every other day⁴. Long times of decalcification, however, significantly contribute to RNA degradation⁶^,⁷^,⁸. To overcome this problem, EDTA concentration was increased to 20%, the pH was raised to 8.0, and the frequency of solution replacement was increased to every 30 min. These conditions, in combination with the large amount of solution to which the tissue is exposed, the vigorous agitation, and the high container/tissue volume ratio, maximized decalcification and reduced treatment times, allowing for a gentle but rapid demineralization. Of note, it is important to mention that when bone tissue samples are to be used for transcriptome sequencing, it may not be necessary to completely decalcify them. In this case, the optimal proportion between enough demineralization and good RNA preservation is to be found. Another important thing to mention is that no matter how samples are treated if they have been fixed, their RNA will be fragmented. The method reported here allows for retainment of the RNA fragments with a size higher than 200 nucleotides (%DV200) (Figure 2F), which indicates high RNA quality⁹^,¹¹.

This method presents certain limitations. First, as mice were the only source of bone tissue samples, the method has been validated only on murine bones, which are relatively small. Moreover, it is not known whether this method can be used for mice older or younger than 8 weeks since it was tested on 8-week-old mice only. We chose 8-week-old mice because they are skeletally mature. As aging modifies the mineral content of bones, changes to this approach may have to be implemented.

Additionally, guidelines are reported to help improve the quality of the tissue sections when FFPE samples of small undecalcified bone specimens are utilized, like, for example, when they are directly collected from tissue banks. In these situations, nothing can be done if RNA is degraded, but section quality can be improved. On the other hand, for samples with good RNA content, such as those shown here, spatial transcriptomic analysis is possible if the provided guidelines are followed. Of note, in primary osteosarcoma specimens, bone structure can be altered by the presence of the tumor mass, making the actual samples weaker and brittle, which may facilitate the sectioning. Therefore, Goldner's Trichrome staining was utilized to assess whether this was the case since mineralized and non-mineralized areas can be identified with this staining technique (Figure 3C).

In conclusion, the reported method represents an easily applicable method to decalcify bone tissue samples and obtain FFPE sections that may effectively be used for NGS or other techniques that require RNA integrity. In addition, guidelines are provided for sectioning samples that may not have been demineralized prior to paraffin embedding, like samples obtained from tissue banks. Given the rapid development of spatial transcriptomics analyses, the proposed method and guidelines may be very helpful in bone research in general and in bone cancer research as well.

Divulgazioni

The authors have nothing to disclose.

Acknowledgements

This work was supported by funds from the Pittsburgh Cure Sarcoma (PCS) and the Osteosarcoma Institute (OSI).

Materials

Advanced orbital shaker	VWR	76683-470	Use to keep tissues under agitation during incubation as reported in the method instructions.
Camel Hair Brushes	Ted Pella	11859	Use to handle FFPE sections as reported in the guidelines.
Dual Index Kit TS Set A 96 rxns	10X Genomics	PN-1000251	Use to perform spatial transcriptomics.
Ethanol 200 Proof	Decon Labs Inc	2701	Use to perform tissue dehydration as reported in the method instructions.
Ethylenediaminetetraacetic Acid, Disodium Salt Dihydrate (EDTA)	Thermo Fisher Scientific	S312-500	Use to prepare EDTA 20% pH 8.0.
Fisherbrand Curved Medium Point General Purpose Forceps	Fisher Scientific	16-100-110	Use to handle FFPE sections as reported in the guidelines.
Fisherbrand Fine Precision Probe	Fisher Scientific	12-000-153	Use to handle FFPE sections as reported in the guidelines.
Fisherbrand Superfrost Plus Microscope Slides	Fisher Scientific	12-550-15	Use to attach sectioned scrolls as reported in the guidelines.
High profile diamond microtome blades	CL Sturkey	D554DD	Use to section FFPE blocks as reported in the guidelines.
Novaseq 150PE	Novogene	N/A	Sequencer.
Paraformaldehyde (PFA) 32% Aqueous Solution EM Grade	Electron Microscopy Sciences	15714-S	Dilute to final concentration of 4% with 1x PBS to perform tissue fixation.
Phosphate buffered saline (PBS)	Thermo Fisher Scientific	10010-049	Ready to use. Use to dilute PFA and to perform washes as reported in the method instructions.
Premiere Tissue Floating Bath	Fisher Scientific	A84600061	Use to remove wrinkles from FFPE sections as reported in the guidelines.
RNase AWAY Surface Decontaminant	Thermo Fisher Scientific	7002	Use to clean all surfaces as reported in the method instructions.
RNeasy DSP FFPE Kit	Qiagen	73604	Use to isolate RNA from FFPE sections once they have been generated as reported in the guidelines.
Semi-Automated Rotary Microtome	Leica Biosystems	RM2245	Use to section FFPE blocks as reported in the guidelines.
Sodium hydroxide	Millipore Sigma	S8045-500	Prepare 10 N solution by slowly dissolving 400 g in 1 liter of Milli-Q water.
Space Ranger	10X Genomics	2.0.1	Use to process sequencing data output .
Surgipath Paraplast	Leica Biosystems	39601006	Use to perform tissue infliltration and embedding as reported in the method instructions.
Visium Accessory Kit	10X Genomics	PN-1000194	Use to perform spatial transcriptomic experiments.
Visium Human Transcriptome Probe Kit Small	10X Genomics	PN-1000363	Use to perform spatial transcriptomic experiments.
Visium Spatial Gene Expression Slide Kit 4 rxns	10X Genomics	PN-1000188	Use to place the sections if performing spatial transcriptomic experiments.
Xylene	Leica Biosystems	3803665	Use to perform tissue clearing as reported in the method instructions.

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Mancinelli, L., Schoedel, K. E., Weiss, K. R., Intini, G. Methods to Enable Spatial Transcriptomics of Bone Tissues. J. Vis. Exp. (207), e66850, doi:10.3791/66850 (2024).