Tissue-specific cell sorting from Drosophila embryos: Application to gene expression analysis

Abstract Melanocyte stem cells (MeSCs) are crucial for generating mature melanocytes that colour the skin and hair. Dysfunction of MeSCs can result in conditions such as hair greying, hypo- or hyper-pigmentation disorders, and melanoma. Here we describe a fluorescence-activated cell sorting (FACS) strategy for isolating MeSCs from mouse skin. The isolated MeSCs can be used in a multitude of experiments including gene expression analysis, transplantation, and others.

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Tissue specific muscle extracellular matrix hydrogel improves skeletal muscle regeneration in vivo over non-matched tissue source

10.1101/2020.06.30.181164 ◽

2020 ◽

Author(s):

Jessica L. Ungerleider ◽

Monika Dzieciatkowska ◽

Kirk C. Hansen ◽

Karen L. Christman

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Extracellular Matrix ◽

Regenerative Medicine ◽

Expression Analysis ◽

Muscle Regeneration ◽

Gene Expression Analysis ◽

Skeletal Muscle Regeneration ◽

Cross Sectional ◽

Tissue Specific

AbstractDecellularized extracellular matrix (ECM) hydrogels present a novel, clinical intervention for a myriad of regenerative medicine applications. The source of ECM is typically the same tissue to which the treatment is applied; however, the need for tissue specific ECM sources has not been rigorously studied. We hypothesized that tissue specific ECM would improve regeneration through preferentially stimulating physiologically relevant processes (e.g. progenitor cell proliferation and differentiation). One of two decellularized hydrogels (tissue specific skeletal muscle or non mesoderm-derived lung) or saline were injected intramuscularly two days after notexin injection in mice (n=7 per time point) and muscle was harvested at days 5 and 14 for histological and gene expression analysis. Both injectable hydrogels were decellularized using the same detergent and were controlled for donor characteristics (i.e. species, age). At day 5, the skeletal muscle ECM hydrogel significantly increased the density of Pax7+ satellite cells in the muscle. Gene expression analysis at day 5 showed that skeletal muscle ECM hydrogels increased expression of genes implicated in muscle contractility. By day 14, skeletal muscle ECM hydrogels improved muscle regeneration over saline and lung ECM hydrogels as shown through a shift in fiber cross sectional area distribution towards larger fibers. This data indicates a potential role for muscle-specific regenerative capacity of decellularized, injectable muscle hydrogels. Further transcriptomic analysis of whole muscle mRNA indicates the mechanism of tissue specific ECM-mediated tissue repair may be immune and metabolism pathway-driven. Taken together, this suggests there is benefit in using tissue specific ECM for regenerative medicine applications.

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Comparative gene expression analysis of the fmnl family of formins during zebrafish development and implications for tissue specific functions

Gene Expression Patterns ◽

10.1016/j.gep.2012.09.002 ◽

2013 ◽

Vol 13 (1-2) ◽

pp. 30-37 ◽

Cited By ~ 5

Author(s):

Adrián Santos-Ledo ◽

Andreas Jenny ◽

Florence L. Marlow

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Tissue Specific ◽

Zebrafish Development

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Fluorescence Activated Cell Sorting (FACS) and Gene Expression Analysis of Fos-expressing Neurons from Fresh and Frozen Rat Brain Tissue

Journal of Visualized Experiments ◽

10.3791/54358 ◽

2016 ◽

Cited By ~ 5

Author(s):

F. Javier Rubio ◽

Xuan Li ◽

Qing-Rong Liu ◽

Raffaello Cimbro ◽

Bruce T. Hope

Keyword(s):

Gene Expression ◽

Rat Brain ◽

Brain Tissue ◽

Expression Analysis ◽

Cell Sorting ◽

Gene Expression Analysis ◽

Fluorescence Activated Cell Sorting ◽

Rat Brain Tissue

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Reference Gene Selection for Normalizing Gene Expression in Ips Sexdentatus (Coleoptera: Curculionidae: Scolytinae) Under Different Experimental Conditions

Frontiers in Physiology ◽

10.3389/fphys.2021.752768 ◽

2021 ◽

Vol 12 ◽

Author(s):

Gothandapani Sellamuthu ◽

Shan Amin ◽

Jan Bílý ◽

Jirí Synek ◽

Roman Modlinger ◽

...

Keyword(s):

Gene Expression ◽

Reference Gene ◽

Expression Analysis ◽

Reference Genes ◽

Gene Expression Analysis ◽

Gene Selection ◽

Experimental Conditions ◽

Tissue Specific ◽

Reference Gene Selection ◽

Ips Sexdentatus

Ips sexdentatus (Coleoptera: Curculionidae: Scolytinae) is one of the most destructive and economically important forest pests. A better understanding of molecular mechanisms underlying its adaptation to toxic host compounds may unleash the potential for future management of this pest. Gene expression studies could be considered as one of the key experimental approaches for such purposes. A suitable reference gene selection is fundamental for quantitative gene expression analysis and functional genomics studies in I. sexdentatus. Twelve commonly used reference genes in Coleopterans were screened under different experimental conditions to obtain accurate and reliable normalization of gene expression data. The majority of the 12 reference genes showed a relatively stable expression pattern among developmental stages, tissue-specific, and sex-specific stages; however, some variabilities were observed during varied temperature incubation. Under developmental conditions, the Tubulin beta-1 chain (β-Tubulin) was the most stable reference gene, followed by translation elongation factor (eEF2) and ribosomal protein S3 (RPS3). In sex-specific conditions, RPS3, β-Tubulin, and eEF2 were the most stable reference genes. In contrast, different sets of genes were shown higher stability in terms of expression under tissue-specific conditions, i.e., RPS3 and eEF2 in head tissue, V-ATPase-A and eEF2 in the fat body, V-ATPase-A and eEF2 in the gut. Under varied temperatures, β-Tubulin and V-ATPase-A were most stable, whereas ubiquitin (UbiQ) and V-ATPase-A displayed the highest expression stability after Juvenile Hormone III treatment. The findings were validated further using real-time quantitative reverse transcription PCR (RT-qPCR)-based target gene expression analysis. Nevertheless, the present study delivers a catalog of reference genes under varied experimental conditions for the coleopteran forest pest I. sexdentatus and paves the way for future gene expression and functional genomic studies on this species.

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Tissue-specific gene expression analysis of silkworm (Bombyx mori) by quantitative real-time RT-PCR

BMB Reports ◽

10.5483/bmbrep.2010.43.7.480 ◽

2010 ◽

Vol 43 (7) ◽

pp. 480-484 ◽

Cited By ~ 6

Author(s):

Seung-Won Park ◽

Seok-Woo Kang ◽

Tae-Won Goo ◽

Seong-Ryul Kim ◽

Gwang-Gill Lee ◽

...

Keyword(s):

Gene Expression ◽

Bombyx Mori ◽

Real Time ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Specific Gene ◽

Rt Pcr ◽

Tissue Specific ◽

Tissue Specific Gene ◽

Silkworm Bombyx Mori

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TEnGExA: an R package based tool for tissue enrichment and gene expression analysis

Briefings in Bioinformatics ◽

10.1093/bib/bbaa221 ◽

2020 ◽

Author(s):

Hukam C Rawal ◽

Ulavappa Angadi ◽

Tapan Kumar Mondal

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Gene Expression Analysis ◽

High Throughput Sequencing ◽

Gene List ◽

Enrichment Analysis ◽

R Package ◽

Web Interface ◽

Tissue Specific ◽

Downstream Analysis

Abstract RNA-seq data analysis with rapidly advancing high-throughput sequencing technology, nowadays provides large number of transcripts or genes to perform downstream analysis including functional annotation and pathway analysis. However for the data from multiple tissues, downstream analysis with tissue-specific or tissue-enriched transcripts is highly preferable. However, there is still a need of tool for quickly performing tissue-enrichment and gene expression analysis irrespective of number of input genes or tissues at various fragments per kilobase of transcript per million fragments mapped (FPKM) thresholds. To fulfill this need, we presented a freely available R package and web-interface tool, TEnGExA, which allows tissue-enrichment analysis (TEA) for any number of genes or transcripts for any species provided only a read-count or FPKM-value matrix as input. Based on the different FPKM value and fold thresholds, TEnGExA classifies the user provided gene lists into tissue-enriched or tissue-specific transcripts along with other standard classes. By analyzing the published sample data from human, plant and microorganism, we signifies that TEnGExA can easily handle complex or large data from any species to provided tissue-enriched gene list for downstream analysis in quick time. In summary, TEnGExA is quick, easy to use and an efficient tool for TEA. The R package is freely available at https://github.com/ubagithub/TEnGExA/ and the GUI web interface is accessible at http://webtom.cabgrid.res.in/tissue_enrich/.

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