Production of RNA for Transcriptomic Analysis from Mouse Spinal Cord Motor Neuron Cell Bodies by Laser Capture Microdissection

Bandyopadhyay, Urmi; Fenton, Wayne A.; Horwich, Arthur L.; Nagy, Mária

doi:10.3791/51168

Cited by 7 publications

(3 citation statements)

References 11 publications

(9 reference statements)

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“…constructed the expression profiling of motor neurons in mouse spinal cord by LCM and microarray. This study prompts our understanding of transcriptional changes in spinal cord motor neurons during neurogenic and neurodegenerative diseases (Bandyopadhyay et al 2014 ). More examples of down-stream utilization of LCM are overviewed elsewhere (Datta et al 2015 ).…”

Section: Technologies Based On Isolation Through Microdissection or P...supporting

confidence: 55%

Spatial transcriptomics: new dimension of understanding biological complexity

Li¹,

Peng²

2022

Biophysics Reports

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Cells and tissues are exquisitely organized in a complex but ordered manner to form organs and bodies so that individuals can function properly. The spatial organization and tissue architecture represent a keynote property underneath all living organisms. Molecular architecture and cellular composition within intact tissues play a vital role in a variety of biological processes, such as forming the complicated tissue functionality, precise regulation of cell transition in all living activities, consolidation of central nervous system, cellular responses to immunological and pathological cues. To explore these biological events at a large scale and fine resolution, a genome-wide understanding of spatial cellular changes is essential. However, previous bulk RNA sequencing and single-cell RNA sequencing technologies could not obtain the important spatial information of tissues and cells, despite their ability to detect high content transcriptional changes. These limitations have prompted the development of numerous spatially resolved technologies which provide a new dimension to interrogate the regional gene expression, cellular microenvironment, anatomical heterogeneity and cell-cell interactions. Since the advent of spatial transcriptomics, related works that use these technologies have increased rapidly, and new methods with higher throughput and resolution have grown quickly, all of which hold great promise to accelerate new discoveries in understanding the biological complexity. In this review, we briefly discussed the historical evolution of spatially resolved transcriptome. We broadly surveyed the representative methods. Furthermore, we summarized the general computational analysis pipeline for the spatial gene expression data. Finally, we proposed perspectives for technological development of spatial multi-omics.

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Section: Technologies Based On Isolation Through Microdissection or P...supporting

confidence: 55%

Spatial transcriptomics: new dimension of understanding biological complexity

Li¹,

Peng²

2022

Biophysics Reports

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“…For example, precise spatial transcriptomic profiling of mouse motor neurons and human postmortem tissues was conducted using LCM coupled with smart-seq2. The study demonstrated that scRNA-seq was feasible with a 62% success rate by LCM-seq, exhibiting considerable facility in different circumstances [47,50]. Moreover, another team proposed geographical position sequencing (GEO-seq) [51,52], which allowed profiling of whole transcriptomes from a small number of cells while preserving their native spatial locations by utilizing an identified list of key genes (zip-code genes) to map cells back to their origins (Figure 2B).…”

Section: Lcm-based Approachesmentioning

confidence: 99%

Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics

Liao

Shao

et al. 2021

Trends in Biotechnology

175

150

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Revealing fine-scale cellular heterogeneity among spatial context and the functional and structural foundations of tissue architecture is fundamental within biological research and pharmacology. Unlike traditional approaches involving single molecules or bulk omics, cutting-edge, spatially resolved transcriptomics techniques offer near-single-cell or even subcellular resolution within tissues. Massive information across higher dimensions along with position-coordinating labels can better map the whole 3D transcriptional landscape of tissues. In this review, we focus on developments and strategies in spatially resolved transcriptomics, compare the cell and gene throughput and spatial resolution in detail for existing methods, and highlight the enormous potential in biomedical research.

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“…Instead, tweaking subtype-specific effector molecules may be a powerful strategy to regenerate functional MNs in fully developed adults. The identification of additional effectors can be achieved in two ways: (i) oriented investigation of downstream targets of known intrinsic regulators such as LIM and/or HOX proteins for example and (ii) unbiased screenings combining, viral retrograde tracing (Stepien et al, 2010 ; Tripodi et al, 2011 ), laser capture micro-dissection (Bandyopadhyay et al, 2014 ) and RNA sequencing (Enjin et al, 2010 ). Such approaches would indubitably unveil new regulators and effectors of SpMN subtype specification.…”

Section: Generation Of Spinal Motor Neuronsmentioning

confidence: 99%

Motor neurons and the generation of spinal motor neuron diversity

Stifani

2014

Front. Cell. Neurosci.

255

247

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Motor neurons (MNs) are neuronal cells located in the central nervous system (CNS) controlling a variety of downstream targets. This function infers the existence of MN subtypes matching the identity of the targets they innervate. To illustrate the mechanism involved in the generation of cellular diversity and the acquisition of specific identity, this review will focus on spinal MNs (SpMNs) that have been the core of significant work and discoveries during the last decades. SpMNs are responsible for the contraction of effector muscles in the periphery. Humans possess more than 500 different skeletal muscles capable to work in a precise time and space coordination to generate complex movements such as walking or grasping. To ensure such refined coordination, SpMNs must retain the identity of the muscle they innervate. Within the last two decades, scientists around the world have produced considerable efforts to elucidate several critical steps of SpMNs differentiation. During development, SpMNs emerge from dividing progenitor cells located in the medial portion of the ventral neural tube. MN identities are established by patterning cues working in cooperation with intrinsic sets of transcription factors. As the embryo develop, MNs further differentiate in a stepwise manner to form compact anatomical groups termed pools connecting to a unique muscle target. MN pools are not homogeneous and comprise subtypes according to the muscle fibers they innervate. This article aims to provide a global view of MN classification as well as an up-to-date review of the molecular mechanisms involved in the generation of SpMN diversity. Remaining conundrums will be discussed since a complete understanding of those mechanisms constitutes the foundation required for the elaboration of prospective MN regeneration therapies.

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Production of RNA for Transcriptomic Analysis from Mouse Spinal Cord Motor Neuron Cell Bodies by Laser Capture Microdissection

Cited by 7 publications

References 11 publications

Spatial transcriptomics: new dimension of understanding biological complexity

Spatial transcriptomics: new dimension of understanding biological complexity

Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics

Motor neurons and the generation of spinal motor neuron diversity

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