popsicleR: A R Package for Pre-processing and Quality Control Analysis of Single Cell RNA-seq Data

Grandi, Francesco; Caroli, Jimmy; Romano, Oriana; Marchionni, Matteo; Forcato, Mattia; Bicciato, Silvio

doi:10.1016/j.jmb.2022.167560

Cited by 13 publications

(5 citation statements)

References 23 publications

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“…New Seurat objects were generated, filtered, and clustered using the PopsicleR package for the E15.5 and P1 maxillary molar datasets ( Grandi et al, 2022 ). We followed the standard workflow, filtering out cells with less than 200 features and more than 6,500 (E15.5) or 7,500 (P1), >20% (E15.5) or 25% (P1) mitochondrial, and >50% (E15.5) or 45% (P1) ribosomal genes.…”

Section: Methodsmentioning

confidence: 99%

Profiles of Wnt pathway gene expression during tooth morphogenesis

Raju,

Piña,

Roth

et al. 2024

Front. Physiol.

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Mouse and human genetic studies indicate key roles of the Wnt10a ligand in odontogenesis. Previous studies have identified effectors and regulators of the Wnt signaling pathway actively expressed during key stages of tooth morphogenesis. However, limitations in multiplexing and spatial resolution hindered a more comprehensive analysis of these signaling molecules. Here, profiling of transcriptomes using fluorescent multiplex in situ hybridization and single-cell RNA-sequencing (scRNA-seq) provide robust insight into the synchronized expression patterns of Wnt10a, Dkk1, and Sost simultaneously during tooth development. First, we identified Wnt10a transcripts restricted to the epithelium at the stage of tooth bud morphogenesis, contrasting that of Sost and Dkk1 localization to the dental mesenchyme. By embryonic day 15.5 (E15.5), a marked shift of Wnt10a expression from dental epithelium to mesenchyme was noted, while Sost and Dkk1 expression remained enriched in the mesenchyme. By postnatal day 0 (P0), co-localization patterns of Wnt10a, Dkk1, and Sost were observed in both terminally differentiating and secreting odontoblasts of molars and incisors. Interestingly, Wnt10a exhibited robust expression in fully differentiated ameloblasts at the developing cusp tip of both molars and incisors, an observation not previously noted in prior studies. At P7 and 14, after the mineralization of dentin and enamel, Wnt10a expression was limited to odontoblasts. Meanwhile, Wnt modulators showed reduced or absent signals in molars. In contrast, strong signals persisted in ameloblasts (for Wnt10a) and odontoblasts (for Wnt10a, Sost, and Dkk1) towards the proximal end of incisors, near the cervical loop. Our scRNA-seq analysis used CellChat to further contextualize Wnt pathway-mediated communication between cells by examining ligand-receptor interactions among different clusters. The co-localization pattern of Wnt10a, Dkk1, and Sost in both terminally differentiating and secreting odontoblasts of molars and incisors potentially signifies the crucial ligand-modulator interaction along the gradient of cytodifferentiation starting from each cusp tip towards the apical region. These data provide cell type-specific insight into the role of Wnt ligands and mediators during epithelial-mesenchymal interactions in odontogenesis.

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Section: Methodsmentioning

confidence: 99%

Profiles of Wnt pathway gene expression during tooth morphogenesis

Raju,

Piña,

Roth

et al. 2024

Front. Physiol.

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“…Single-cell RNA-sequencing and Visium datasets were primarily processed with Seurat functionality, while Xenium was analyzed according to Giotto vignettes. Other packages used for pre-processing and visualization included PopsicleR (Grandi et al, 2022), Giotto (Dries et al, 2021), and SCpubr (Blanco-Carmona, 2022). Up to date code is located at github.com/dmartaroth.…”

Section: Methodsmentioning

confidence: 99%

Tendon-associated gene expression precedes osteogenesis in mid-palatal suture establishment

Roth,

Oliver Piña,

Raju

et al. 2024

Preprint

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Orthodontic maxillary expansion relies on intrinsic mid-palatal suture mechanobiology to induce guided osteogenesis, yet establishment of the mid-palatal suture within the continuous secondary palate and causes of maxillary insufficiency remain poorly understood. In contrast, advances in cranial suture research hold promise to improve surgical repair of prematurely fused cranial sutures in craniosynostosis to potentially restore the obliterated signaling environment and ensure continual success of the intervention. We hypothesized that mid-palatal suture establishment is governed by shared principles with calvarial sutures and involves functional linkage between expanding primary ossification centres with the midline mesenchyme. We characterized establishment of the mid-palatal suture from late embryonic to early postnatal timepoints. Suture establishment was visualized using histological techniques and multimodal transcriptomics. We identified that mid-palatal suture formation depends on a spatiotemporally controlled signalling milieu in which tendon-associated genes play a significant role. We mapped relationships between extracellular matrix-encoding gene expression, tenocyte markers, and novel suture patency candidate genes. We identified similar expression patterns in FaceBase-deposited scRNA-seq datasets from cranial sutures. These findings demonstrate shared biological principles for suture establishment, providing further avenues for future development and understanding of maxillofacial interventions.

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“…However, the wealth of biological insights embedded in scRNA-seq data has led to a constant influx of new computational tools, creating a challenge for investigators to stay abreast of the latest advancements in this rapidly evolving landscape of tools and analysis steps. Many existing workflows for scRNA-seq data processing are either no longer actively maintained or lack essential steps necessary for comprehensive scRNA-seq analysis, such as the conversion of sequencer binary base call (BCL) files into human-readable text format (FASTQ files) or read alignment ( Grandi et al 2022 , Prieto et al 2022 , Rich-Griffin et al 2023 ), as well as robust cell type identification ( Garcia-Jimeno et al 2022 ). Furthermore, the computational complexity associated with most available workflows often presents a significant barrier, restricting their usage to investigators possessing advanced computational skills ( Rich-Griffin et al 2023 ).…”

Section: Introductionmentioning

confidence: 99%

Scaling up single-cell RNA-seq data analysis with CellBridge workflow

Nouri,

Kurlovs,

Gaglia

et al. 2023

Bioinformatics

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Summary Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression at the individual cell level, unraveling unprecedented insights into cellular heterogeneity. However, the analysis of scRNA-seq data remains a challenging and time-consuming task, often demanding advanced computational expertise, rendering it impractical for high-volume environments and applications. We present CellBridge, an automated workflow designed to simplify the standard procedures entailed in scRNA-seq data analysis, eliminating the need for specialized computational expertise. CellBridge utilizes state-of-the-art computational methods, integrating a range of advanced functionalities, covering the entire process from raw unaligned sequencing reads to cell type annotation. Hence, CellBridge accelerates the pace of discovery by seamlessly enabling insights into vast volumes of scRNA-seq data, without compromising workflow control and reproducibility. Availability and implementation The source code, detailed documentation, and materials required to reproduce the results are available on GitHub and archived in Zenodo. For the CellBridge pre-processing step (v1.0.0), access the GitHub repository at https://github.com/Sanofi-Public/PMCB-ToBridge and the Zenodo archive at https://zenodo.org/records/10246161. For the CellBridge processing step (v1.0.0), visit the GitHub repository at https://github.com/Sanofi-Public/PMCB-CellBridge and the Zenodo archive at https://zenodo.org/records/10246046.

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popsicleR: A R Package for Pre-processing and Quality Control Analysis of Single Cell RNA-seq Data

Cited by 13 publications

References 23 publications

Profiles of Wnt pathway gene expression during tooth morphogenesis

Profiles of Wnt pathway gene expression during tooth morphogenesis

Tendon-associated gene expression precedes osteogenesis in mid-palatal suture establishment

Scaling up single-cell RNA-seq data analysis with CellBridge workflow

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