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Adult Stem Cells01:33

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Stem cells are undifferentiated cells that divide and produce more stem cells or progenitor cells that differentiate into mature, specialized cell types. All the cells in the body are generated from stem cells in the early embryo, but small populations of stem cells are also present in many adult tissues including the bone marrow, brain, skin, and gut. These adult stem cells typically produce the various cell types found in that tissue—to replace cells that are damaged or to continuously...
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Embryonic stem (ES) cells were first discovered in mice in 1981 by Martin Evans. In 1998, James Thomson identified a method to isolate embryonic stem cells from humans. Human embryonic stem cells (hESCs) are obtained from 3-5 day old embryos that remain unused after an in vitro fertilization procedure.
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Stem cells are undifferentiated cells that divide and produce different types of cells. Ordinarily, cells that have differentiated into a specific cell type are post-mitotic—that is, they no longer divide. However, scientists have found a way to reprogram these mature cells so that they “de-differentiate” and return to an unspecialized, proliferative state. These cells are also pluripotent like embryonic stem cells—able to produce all cell types—and are therefore...
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A variable, usually notated by capital letters such as X and Y, is a characteristic or measurement that can be determined for each member of a population. Data are the actual values of variables. They may be numbers, or they may be words. Datum is a single value.
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Stemformatics: visualize and download curated stem cell data.

Jarny Choi1, Chris M Pacheco1, Rowland Mosbergen1

  • 1Centre for Stem Cell Systems, Anatomy and Neuroscience, The University of Melbourne, Melbourne, Victoria 3010, Australia.

Nucleic Acids Research
|November 9, 2018
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Summary
This summary is machine-generated.

Stemformatics is a gene expression data portal for stem cell research, offering high-quality, consistently processed datasets and intuitive tools for data exploration and comparison. It aids in identifying cell-type specific genes.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Stem Cell Biology

Background:

  • Established gene expression data portal serving the stem cell research community.
  • Contains over 420 public datasets from microarray, RNA sequencing, and single-cell profiling.
  • Focuses on pluripotency, tissue stem cells, and developmental processes.

Purpose of the Study:

  • To provide a curated and quality-controlled repository of gene expression data for stem cell research.
  • To offer biologists intuitive tools for data exploration and cross-dataset comparisons.
  • To facilitate the identification of cell-type restricted and housekeeping genes.

Main Methods:

  • Stringent quality control metrics and proprietary pipelines for dataset processing.
  • Selection of handpicked datasets from raw files, with approximately 30% failing quality control.
  • Development of user-friendly tools for visual data exploration, including PCA plots and hierarchical clustering.

Main Results:

  • Ensured high data quality and consistent processing across all datasets on the portal.
  • Provided interactive tools for visualizing gene expression profiles and performing cross-dataset comparisons.
  • Facilitated the identification of cell-type specific genes and potential housekeeping genes.

Conclusions:

  • Stemformatics offers a valuable, high-quality resource for stem cell researchers.
  • The portal's tools empower biologists to effectively explore and analyze complex gene expression data.
  • Consistent data processing and quality control enhance the reliability of research findings.