Computational Sequence Design Techniques for DNA Microarray Technologies

In systems biology and biomedical research, microarray technology is a method of choice that enables the complete quantitative and qualitative ascertainment of gene expression patterns for whole genomes. The selection of high quality oligonucleotide sequences that behave consistently across multiple experiments is a key step in the design, fabrication and experimental performance of DNA microarrays. The aim of this chapter is to outline recent algorithmic developments in microarray probe design, evaluate existing probe sequences used in commercial arrays, and suggest methodologies that have the potential to improve on existing design techniques.

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Computational Sequence Design Techniques for DNA Microarray Technologies

Bioinformatics ◽

10.4018/978-1-4666-3604-0.ch048 ◽

2013 ◽

pp. 884-918

Author(s):

Dan Tulpan ◽

Athos Ghiggi ◽

Roberto Montemanni

Keyword(s):

Dna Microarrays ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Probe Design ◽

High Quality ◽

Microarray Probe ◽

Experimental Performance ◽

Whole Genomes ◽

Selection Of ◽

Design Techniques

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RNA In Situ Hybridization for Detecting Gene Expression Patterns in the Abdomens and Wings of Drosophila Species

Methods and Protocols ◽

10.3390/mps4010020 ◽

2021 ◽

Vol 4 (1) ◽

pp. 20

Author(s):

Mujeeb Shittu ◽

Tessa Steenwinkel ◽

William Dion ◽

Nathan Ostlund ◽

Komal Raja ◽

...

Keyword(s):

Gene Expression ◽

In Situ Hybridization ◽

Expression Patterns ◽

Drosophila Species ◽

Gene Expression Patterns ◽

Probe Design ◽

Tissue Preparation ◽

Design And Synthesis ◽

Rna In Situ Hybridization

RNA in situ hybridization (ISH) is used to visualize spatio-temporal gene expression patterns with broad applications in biology and biomedicine. Here we provide a protocol for mRNA ISH in developing pupal wings and abdomens for model and non-model Drosophila species. We describe best practices in pupal staging, tissue preparation, probe design and synthesis, imaging of gene expression patterns, and image-editing techniques. This protocol has been successfully used to investigate the roles of genes underlying the evolution of novel color patterns in non-model Drosophila species.

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A Method for Cryopreservation and Single Nucleus RNA-sequencing of Normal Adult Human Interventricular Septum Heart Tissue Reveals Cellular Diversity and Function

10.21203/rs.3.rs-136136/v1 ◽

2020 ◽

Author(s):

Amy Larson ◽

Michael T. Chin

Keyword(s):

Single Cell ◽

Human Heart ◽

Expression Patterns ◽

Interventricular Septum ◽

Cell Types ◽

Heart Tissue ◽

Gene Expression Patterns ◽

High Quality ◽

Normal Human ◽

Human Heart Tissue

Abstract Background: Single cell sequencing of human heart tissue is technically challenging and methods to cryopreserve heart tissue for obtaining single cell information have not been standardized. Studies published to date have used varying methods to preserve and process human heart tissue, and have generated interesting datasets, but development of a biobanking standard has not yet been achieved. Heart transcription patterns are known to be regionally diverse, and there are few single cell datasets for normal human heart tissue. Methods: Using pig tissue, we developed a rigorous and reproducible method for tissue mincing and cryopreservation that allowed recovery of high quality single nuclei RNA. We subsequently tested this protocol on normal human heart tissue obtained from organ donors and were able to recover high quality nuclei for generation of single nuclei RNA-seq datasets, using a commercially available platform from 10x Genomics. We analyzed these datasets using standard software packages such as CellRanger and Seurat. Results: Human heart tissue preserved with our method consistently yielded nuclear RNA with RNA Integrity Numbers of greater than 8.5. We demonstrate the utility of this method for single nuclei RNA-sequencing of the normal human interventricular septum and delineating its cellular diversity. The human IVS showed unexpected diversity with detection of 23 distinct cell clusters that were subsequently categorized into different cell types. Cardiomyocytes and fibroblasts were the most commonly identified cell types and could be further subdivided into 5 different cardiomyocyte subtypes and 6 different fibroblast subtypes that differed by gene expression patterns. Ingenuity Pathway analysis of these gene expression patterns suggested functional diversity in these cell subtypes. Conclusions: Here we report a simple technical method for cryopreservation and subsequent nuclear isolation of human interventricular septum tissue that can be done with common laboratory equipment. We show how this method can be used to generate single nuclei transcriptomic datasets that rival those already published by larger groups in terms of cell diversity and complexity and suggest that this simple method can provide guidance for biobanking of human myocardial tissue for complex genomic analysis.

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Gravitational Singularities in Particle Swarms. Application to the Discovery of Gene Expression Patterns in DNA Microarrays.

Evolutionary Computation ◽

10.5772/9600 ◽

2009 ◽

Author(s):

Gerard Ramstein

Keyword(s):

Gene Expression ◽

Dna Microarrays ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Particle Swarms

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A method for cryopreservation and single nucleus RNA-sequencing of normal adult human interventricular septum heart tissue reveals cellular diversity and function

BMC Medical Genomics ◽

10.1186/s12920-021-01011-z ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Amy Larson ◽

Michael T. Chin

Keyword(s):

Single Cell ◽

Human Heart ◽

Expression Patterns ◽

Interventricular Septum ◽

Cell Types ◽

Heart Tissue ◽

Gene Expression Patterns ◽

High Quality ◽

Normal Human ◽

Human Heart Tissue

Abstract Background Single cell sequencing of human heart tissue is technically challenging and methods to cryopreserve heart tissue for obtaining single cell information have not been standardized. Studies published to date have used varying methods to preserve and process human heart tissue, and have generated interesting datasets, but development of a biobanking standard has not yet been achieved. Heart transcription patterns are known to be regionally diverse, and there are few single cell datasets for normal human heart tissue. Methods Using pig tissue, we developed a rigorous and reproducible method for tissue mincing and cryopreservation that allowed recovery of high quality single nuclei RNA. We subsequently tested this protocol on normal human heart tissue obtained from organ donors and were able to recover high quality nuclei for generation of single nuclei RNA-seq datasets, using a commercially available platform from 10× Genomics. We analyzed these datasets using standard software packages such as CellRanger and Seurat. Results Human heart tissue preserved with our method consistently yielded nuclear RNA with RNA Integrity Numbers of greater than 8.5. We demonstrate the utility of this method for single nuclei RNA-sequencing of the normal human interventricular septum and delineating its cellular diversity. The human IVS showed unexpected diversity with detection of 23 distinct cell clusters that were subsequently categorized into different cell types. Cardiomyocytes and fibroblasts were the most commonly identified cell types and could be further subdivided into 5 different cardiomyocyte subtypes and 6 different fibroblast subtypes that differed by gene expression patterns. Ingenuity Pathway analysis of these gene expression patterns suggested functional diversity in these cell subtypes. Conclusions Here we report a simple technical method for cryopreservation and subsequent nuclear isolation of human interventricular septum tissue that can be done with common laboratory equipment. We show how this method can be used to generate single nuclei transcriptomic datasets that rival those already published by larger groups in terms of cell diversity and complexity and suggest that this simple method can provide guidance for biobanking of human myocardial tissue for complex genomic analysis.

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Tolerance at the genetic level of the brine shrimp Artemia salina to a wide range of salinity

10.21203/rs.3.rs-91049/v1 ◽

2020 ◽

Author(s):

JunMo Lee ◽

Jong Soo Park

Keyword(s):

Gene Expression ◽

Brine Shrimp ◽

High Salinity ◽

Transcriptome Assembly ◽

Expression Patterns ◽

Artemia Salina ◽

Gene Expression Patterns ◽

Organic Osmolytes ◽

High Quality ◽

Genetic Level

Abstract Background: The brine shrimp Artemia salina can thrive in a variety of salinities and is commonly distributed in natural hypersaline lakes and solar salterns. The zooplankter A. salina proves to be a filter feeder, consuming the alga Dunaliella and prokaryotes and plays a critical role in the hypersaline food web. However, the high salinity adaptation mechanisms of A. salina remain poorly understood through transcriptome analysis. Here, we examined the gene expression patterns of A. salina adults that were salt-adapted for 2–4 weeks at five salinities (35, 50, 100, 150, and 230 psu), and generated long-read isoform sequencing (IsoSeq) data to construct a high-quality transcriptome assembly of A. salina. The patterns of A. salina along the salinity gradient provide evidence for halotolerant and euryhaline adaptations at the genetic level. Results: We confirmed that the activity of sodium/potassium ATPase was up-regulated at the genetic level in high salinity waters. Interestingly, genes related to beta-mannosidase and mannose activities were also up-regulated, suggesting that mannose and mannose derivatives may be accumulated as organic osmolytes. Alternatively, considering that glucose and galactose-related activities were suppressed at high salinities, mannose may be the primary sugar involved in the glycolytic pathway under such conditions. This result further supports the theory that mannose is the main energy source used by A. salina in highly saline environments. The gene expression patterns of A. salina may also be affected by increased thickness of the cuticle, increased numbers of mitochondria, and low dissolved oxygen in high salinity waters. Furthermore, the cellular response of A. salina to acclimation to intermediate salinities depends on the number and type of genes expressed; differential expression patterns are likely to fluctuate at the population level. Conclusions: Our results provide a high-quality transcriptome assembly of the cosmopolitan brine shrimp Artemia salina at five different salinities (35, 50, 100, 150, and 230 psu) for the first time. The gene expression patterns of salt-adapted A. salina display greater osmoregulation process complexity than we thought. Furthermore, A. salina represents a potential model organism to study locally adapted populations at various salinities.

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Gene Expression Patterns in Ovarian Carcinomas

Molecular Biology of the Cell ◽

10.1091/mbc.e03-05-0279 ◽

2003 ◽

Vol 14 (11) ◽

pp. 4376-4386 ◽

Cited By ~ 227

Author(s):

Marci E. Schaner ◽

Douglas T. Ross ◽

Giuseppe Ciaravino ◽

Therese Sørlie ◽

Olga Troyanskaya ◽

...

Keyword(s):

Gene Expression ◽

Estrogen Receptor ◽

Dna Microarrays ◽

Clear Cell ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Published Data ◽

Breast Cancers ◽

Ovarian Carcinomas ◽

Ovarian Cancers

We used DNA microarrays to characterize the global gene expression patterns in surface epithelial cancers of the ovary. We identified groups of genes that distinguished the clear cell subtype from other ovarian carcinomas, grade I and II from grade III serous papillary carcinomas, and ovarian from breast carcinomas. Six clear cell carcinomas were distinguished from 36 other ovarian carcinomas (predominantly serous papillary) based on their gene expression patterns. The differences may yield insights into the worse prognosis and therapeutic resistance associated with clear cell carcinomas. A comparison of the gene expression patterns in the ovarian cancers to published data of gene expression in breast cancers revealed a large number of differentially expressed genes. We identified a group of 62 genes that correctly classified all 125 breast and ovarian cancer specimens. Among the best discriminators more highly expressed in the ovarian carcinomas were PAX8 (paired box gene 8), mesothelin, and ephrin-B1 (EFNB1). Although estrogen receptor was expressed in both the ovarian and breast cancers, genes that are coregulated with the estrogen receptor in breast cancers, including GATA-3, LIV-1, and X-box binding protein 1, did not show a similar pattern of coexpression in the ovarian cancers.

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