scholarly journals Single-cell transcriptome provides novel insights into antler stem cells, a cell type capable of mammalian organ regeneration

2018 ◽  
Author(s):  
Hengxing Ba ◽  
Datao Wang ◽  
Weiyao Wu ◽  
Hongmei Sun ◽  
Chunyi Li
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Single Cell ◽  
Large Cell ◽  
Stem Cell Markers ◽  
Single Cell Level ◽  
Cell Type ◽  
Cell Level ◽  
Homogeneous Population ◽  
Organ Regeneration

AbstractAntler regeneration, a stem cell-based epimorphic process, has potential as a valuable model for regenerative medicine. A pool of antler stem cells (ASCs) for antler development is located in the antlerogenic periosteum (AP). However, whether this ASC pool is homogenous or heterogeneous has not been fully evaluated. In this study, we produced a comprehensive transcriptome dataset at the single-cell level for the ASCs based on the 10x Genomics platform (scRNA-seq). A total of 4,565 ASCs were sequenced and classified into a large cell cluster, indicating that the ASCs resident in the AP are likely to be a homogeneous population. The scRNA-seq data revealed that tumor-related genes were highly expressed in these homogeneous ASCs: i.e. TIMP1, TMSB10, LGALS1, FTH1, VIM, LOC110126017 and S100A4. Results of screening for stem cell markers suggest that the ASCs may be considered as a special type of stem cell between embryonic (CD9) and adult (CD29, CD90, NPM1 and VIM) stem cells. Our results provide the first comprehensive transcriptome analysis at the single-cell level for the ASCs, and identified only one major cell type resident in the AP and some key stem cell genes, which may hold the key to why antlers, the unique mammalian organ, can fully regenerate once lost.

scholarly journals Crucial stem cell experiments? Stem cells, uncertainty, and single-cell experiments

2015 ◽  
Vol 30 (2) ◽  
pp. 183
Author(s):  
Melinda Fagan
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Single Cell ◽  
Single Cells ◽  
Single Cell Level ◽  
Epistemic Circularity ◽  
Cell Level ◽  
Differentiation Potential ◽  
Self Renewal

I have previously argued that stem cell experiments cannot in principle demonstrate that a single cell is a stem cell ([reference omitted for anonymous review]).  Laplane and others dispute this claim, citing experiments that identify stem cells at the single-cell level.  This paper rebuts the counterexample, arguing that these alleged ‘crucial stem cell experiments’ do not measure self-renewal for a single cell, do not establish a single cell’s differentiation potential, and, if interpreted as providing results about single cells, fall into epistemic circularity.  I then examine the source of the dispute, noting differences in philosophical and experimental perspectives.

scholarly journals Single-Cell Transcriptome Analysis as a Promising Tool to Study Pluripotent Stem Cell Reprogramming

2021 ◽  
Vol 22 (11) ◽  
pp. 5988
Author(s):  
Hyun Kyu Kim ◽  
Tae Won Ha ◽  
Man Ryul Lee
Keyword(s):  
Stem Cells ◽  
Single Cell ◽  
Cell Fate ◽  
Human Cell ◽  
Transcriptome Analysis ◽  
Single Cell Analysis ◽  
Embryonic Stem ◽  
Single Cell Level ◽  
Cell Analysis ◽  
Cell Level

Cells are the basic units of all organisms and are involved in all vital activities, such as proliferation, differentiation, senescence, and apoptosis. A human body consists of more than 30 trillion cells generated through repeated division and differentiation from a single-cell fertilized egg in a highly organized programmatic fashion. Since the recent formation of the Human Cell Atlas consortium, establishing the Human Cell Atlas at the single-cell level has been an ongoing activity with the goal of understanding the mechanisms underlying diseases and vital cellular activities at the level of the single cell. In particular, transcriptome analysis of embryonic stem cells at the single-cell level is of great importance, as these cells are responsible for determining cell fate. Here, we review single-cell analysis techniques that have been actively used in recent years, introduce the single-cell analysis studies currently in progress in pluripotent stem cells and reprogramming, and forecast future studies.

Critical downstream analysis steps for single-cell RNA sequencing data

2021 ◽  
Author(s):  
Zilong Zhang ◽  
Feifei Cui ◽  
Chen Lin ◽  
Lingling Zhao ◽  
Chunyu Wang ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Noisy Data ◽  
Single Cell Level ◽  
Cell Type ◽  
Sequencing Data ◽  
Cell Level ◽  
Bioinformatics Tool ◽  
Single Cell Rna Sequencing ◽  
Downstream Analysis

Abstract Single-cell RNA sequencing (scRNA-seq) has enabled us to study biological questions at the single-cell level. Currently, many analysis tools are available to better utilize these relatively noisy data. In this review, we summarize the most widely used methods for critical downstream analysis steps (i.e. clustering, trajectory inference, cell-type annotation and integrating datasets). The advantages and limitations are comprehensively discussed, and we provide suggestions for choosing proper methods in different situations. We hope this paper will be useful for scRNA-seq data analysts and bioinformatics tool developers.

scholarly journals Signaling Profiling at the Single-Cell Level Identifies a Distinct Signaling Signature in Murine Hematopoietic Stem Cells

Stem Cells ◽  
2012 ◽  
Vol 30 (7) ◽  
pp. 1447-1454 ◽  
Author(s):  
Juan Du ◽  
Jinyong Wang ◽  
Guangyao Kong ◽  
Jing Jiang ◽  
Jingfang Zhang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Hematopoietic Stem Cells ◽  
Single Cell ◽  
Single Cell Level ◽  
Cell Level ◽  
Hematopoietic Stem

scholarly journals Probing the Interaction Forces of Prostate Cancer Cells with Collagen I and Bone Marrow Derived Stem Cells on the Single Cell Level

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e57706 ◽  
Author(s):  
Ediz Sariisik ◽  
Denitsa Docheva ◽  
Daniela Padula ◽  
Cvetan Popov ◽  
Jan Opfer ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Stem Cells ◽  
Bone Marrow ◽  
Single Cell ◽  
Cancer Cells ◽  
Collagen I ◽  
Single Cell Level ◽  
Prostate Cancer Cells ◽  
Cell Level ◽  
Interaction Forces

scholarly journals Resolution of DNA damage at the single-cell level shows largely different actions of X-rays and bleomycin.

1995 ◽  
Vol 43 (2) ◽  
pp. 229-235 ◽  
Author(s):  
M I Affentranger ◽  
W Burkart
Keyword(s):  
Single Cell ◽  
Cell Population ◽  
Large Cell ◽  
Dna Strand Breaks ◽  
Single Cell Level ◽  
X Rays ◽  
Cell Level ◽  
Strand Breaks ◽  
Two Agents ◽  
Dna Strand

Both X-rays and the radiomimetic agent bleomycin (BLM) induce DNA strand breaks, predominantly via reactive radicals. To compare the induction of breaks with the two agents in Chinese hamster (CHO-K1) cells, two different alkaline unwinding methods, a 3H tracer-based analysis of large cell populations and an optical adaption allowing measurement of single cells, were applied. Radiation and BLM show qualitatively similar dose responses when the average number of DNA strand breaks is measured in a large cell population. However, the breakage pattern at the single-cell level indicates large discrepancies between the actions of the two agents. Irradiated cells show a uniform distribution of DNA strand breaks over the cell population. Effects of treatment with 30 micrograms x ml-1 BLM for 2 hr vary from practically zero in some cells to high levels of DNA strand breakage in others. Unlike the repair of radiation-induced DNA breaks, the repair efficiency of BLM-induced DNA strand breaks, as measured at the single-cell level, varies strongly among cells of the same population. Such heterogeneity at the cellular level potentially reduces BLM's usefulness for tumor therapy because the appearance of BLM-resistant subpopulations may critically impair treatment outcome.

scholarly journals Cellular Barcoding Links B-1a B Cell Potential to a Fetal Hematopoietic Stem Cell State at the Single-Cell Level

Immunity ◽  
2016 ◽  
Vol 45 (2) ◽  
pp. 346-357 ◽  
Author(s):  
Trine A. Kristiansen ◽  
Elin Jaensson Gyllenbäck ◽  
Alya Zriwil ◽  
Tomas Björklund ◽  
Jeremy A. Daniel ◽  
...  
Keyword(s):  
Stem Cell ◽  
B Cell ◽  
Single Cell ◽  
Hematopoietic Stem Cell ◽  
Single Cell Level ◽  
Cell Level ◽  
Cell Potential ◽  
Hematopoietic Stem ◽  
Stem Cell State ◽  
Cellular Barcoding

33 Single-Cell Level Analysis Reveals Heterogeneous Expression of Stem-Cell Specific Genes in Human Small Intestinal Organoids

2016 ◽  
Vol 150 (4) ◽  
pp. S11
Author(s):  
Kohei Suzuki ◽  
Satoru Fujii ◽  
Ami Kawamoto ◽  
Fumiaki Ishibashi ◽  
Toru Nakata ◽  
...  
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Single Cell Level ◽  
Cell Level ◽  
Intestinal Organoids ◽  
Heterogeneous Expression ◽  
Small Intestinal ◽  
Level Analysis
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