Stemformatics 数据门户网站实现了实验室衍生髓系细胞的转录基准。

IF 5.9 2区 医学 Q1 CELL & TISSUE ENGINEERING Stem Cell Reports Pub Date : 2024-06-11 Epub Date: 2024-05-23 DOI:10.1016/j.stemcr.2024.04.012
Jarny Choi, Suzanne K Butcher, Paul W Angel, Jack Bransfield, Jake Barry, Noel Faux, Bobbie Shaban, Priyanka Pillai, Aleks Michalewicz, Christine A Wells
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引用次数: 0

摘要

十多年来,Stemformatics.org 一直在为干细胞研究界提供服务,让用户可以轻松查找和查看多能干细胞和成体干细胞及其后代的转录概况,比较来自多种组织和衍生方法的数据。近年来,Stemformatics 已将工作重点从策划转向整理和整合具有共享表型的公共数据。它现在拥有多个基于人类髓系细胞的整合表达图集,可以方便地进行跨数据集比较,发现新出现的细胞亚群和激活特性。这些表达图谱集是为外部用户设计的,他们可以将自己的数据与通用参考数据进行比对。在这里,我们通过案例研究来说明如何查找和探索以前发表的相关数据集,以及如何将体外衍生细胞与集成图集中的细胞进行转录匹配,以突出感兴趣的表型。
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Stemformatics data portal enables transcriptional benchmarking of lab-derived myeloid cells.

Stemformatics.org has been serving the stem cell research community for over a decade, by making it easy for users to find and view transcriptional profiles of pluripotent and adult stem cells and their progeny, comparing data derived from multiple tissues and derivation methods. In recent years, Stemformatics has shifted its focus from curation to collation and integration of public data with shared phenotypes. It now hosts several integrated expression atlases based on human myeloid cells, which allow for easy cross-dataset comparisons and discovery of emerging cell subsets and activation properties. The atlases are designed for external users to benchmark their own data against a common reference. Here, we use case studies to illustrate how to find and explore previously published datasets of relevance and how in-vitro-derived cells can be transcriptionally matched to cells in the integrated atlas to highlight phenotypes of interest.

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来源期刊
Stem Cell Reports
Stem Cell Reports CELL & TISSUE ENGINEERING-CELL BIOLOGY
CiteScore
10.50
自引率
1.70%
发文量
200
审稿时长
28 weeks
期刊介绍: Stem Cell Reports publishes high-quality, peer-reviewed research presenting conceptual or practical advances across the breadth of stem cell research and its applications to medicine. Our particular focus on shorter, single-point articles, timely publication, strong editorial decision-making and scientific input by leaders in the field and a "scoop protection" mechanism are reasons to submit your best papers.
期刊最新文献
Deep-supercooling preservation of stem cell spheroids for chondral defect repairment. Breaking the burst: Unveiling mechanisms behind fragmented network bursts in patient-derived neurons. Transplantation of human pluripotent stem cell-derived retinal sheet in a primate model of macular hole. Accelerated mitochondrial dynamics promote spermatogonial differentiation. Validation of non-destructive morphology-based selection of cerebral cortical organoids by paired morphological and single-cell RNA-seq analyses.
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