scholarly journals RNAlater and flash freezing storage methods nonrandomly influence observed gene expression in RNAseq experiments

2018 ◽  
Author(s):  
Courtney N. Passow ◽  
Thomas J. Y. Kono ◽  
Bethany A. Stahl ◽  
James B. Jaggard ◽  
Alex C. Keene ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liquid Nitrogen ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gc Content ◽  
Gene Expression Profiles ◽  
Expression Studies ◽  
Genome Wide ◽  
Differential Gene ◽  
Genome Wide Gene Expression

AbstractRNA-sequencing is a popular next-generation sequencing technique for assaying genome-wide gene expression profiles. Nonetheless, it is susceptible to biases that are introduced by sample handling prior gene expression measurements. Two of the most common methods for preserving samples in both field-based and laboratory conditions are submersion in RNAlater and flash freezing in liquid nitrogen. Flash freezing in liquid nitrogen can be impractical, particularly for field collections. RNAlater is a solution for stabilizing tissue for longer-term storage as it rapidly permeates tissue to protect cellular RNA. In this study, we assessed genome-wide expression patterns in 30 day old fry collected from the same brood at the same time point that were flash-frozen in liquid nitrogen and stored at −80°C or submerged and stored in RNAlater at room temperature, simulating conditions of fieldwork. We show that sample storage is a significant factor influencing observed differential gene expression. In particular, genes with elevated GC content exhibit higher observed expression levels in liquid nitrogen flash-freezing relative to RNAlater-storage. Further, genes with higher expression in RNAlater relative to liquid nitrogen experience disproportionate enrichment for functional categories, many of which are involved in RNA processing. This suggests that RNAlater may elicit a physiological response that has the potential to bias biological interpretations of expression studies. The biases introduced to observed gene expression arising from mimicking many field-based studies are substantial and should not be ignored.

scholarly journals RankerGUI: A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics

2019 ◽  
Vol 20 (23) ◽  
pp. 6098 ◽  
Author(s):  
Amarinder Singh Thind ◽  
Kumar Parijat Tripathi ◽  
Mario Rosario Guarracino
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Web Application ◽  
Cellular Response ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Experimental Conditions ◽  
Differential Gene

The comparison of high throughput gene expression datasets obtained from different experimental conditions is a challenging task. It provides an opportunity to explore the cellular response to various biological events such as disease, environmental conditions, and drugs. There is a need for tools that allow the integration and analysis of such data. We developed the “RankerGUI pipeline”, a user-friendly web application for the biological community. It allows users to use various rank based statistical approaches for the comparison of full differential gene expression profiles between the same or different biological states obtained from different sources. The pipeline modules are an integration of various open-source packages, a few of which are modified for extended functionality. The main modules include rank rank hypergeometric overlap, enriched rank rank hypergeometric overlap and distance calculations. Additionally, preprocessing steps such as merging differential expression profiles of multiple independent studies can be added before running the main modules. Output plots show the strength, pattern, and trends among complete differential expression profiles. In this paper, we describe the various modules and functionalities of the developed pipeline. We also present a case study that demonstrates how the pipeline can be used for the comparison of differential expression profiles obtained from multiple platforms’ data of the Gene Expression Omnibus. Using these comparisons, we investigate gene expression patterns in kidney and lung cancers.

Acquiring genome-wide gene expression profiles in Guthrie card blood spots using microarrays

2010 ◽  
Vol 61 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Sok Kean Khoo ◽  
Karl Dykema ◽  
Naga Manjari Vadlapatla ◽  
David LaHaie ◽  
Saul Valle ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Guthrie Card ◽  
Blood Spots ◽  
Genome Wide ◽  
Genome Wide Gene Expression

Genome-Wide Differential Gene Expression Profiles in Broiler Chickens with Gangrenous Dermatitis

2012 ◽  
Vol 56 (4) ◽  
pp. 670-679 ◽  
Author(s):  
Duk Kyung Kim ◽  
Hyun S. Lillehoj ◽  
Kyung Woo Lee ◽  
Seung Ik Jang ◽  
Anthony P. Neumann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Broiler Chickens ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Genome Wide ◽  
Differential Gene

scholarly journals Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules

2021 ◽  
Author(s):  
Jakub Jankowski ◽  
Hye Kyung Lee ◽  
Julia Wilflingseder ◽  
Lothar Hennighausen
Keyword(s):  
Gene Expression ◽  
Proximal Tubule ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Regulatory Elements ◽  
Rna Seq ◽  
Angiotensin Converting Enzyme 2 ◽  
Genome Wide ◽  
Cytokine Stimulation

SummaryRecently, a short, interferon-inducible isoform of Angiotensin-Converting Enzyme 2 (ACE2), dACE2 was identified. ACE2 is a SARS-Cov-2 receptor and changes in its renal expression have been linked to several human nephropathies. These changes were never analyzed in context of dACE2, as its expression was not investigated in the kidney. We used Human Primary Proximal Tubule (HPPT) cells to show genome-wide gene expression patterns after cytokine stimulation, with emphasis on the ACE2/dACE2 locus. Putative regulatory elements controlling dACE2 expression were identified using ChIP-seq and RNA-seq. qRT-PCR differentiating between ACE2 and dACE2 revealed 300- and 600-fold upregulation of dACE2 by IFNα and IFNβ, respectively, while full length ACE2 expression was almost unchanged. JAK inhibitor ruxolitinib ablated STAT1 and dACE2 expression after interferon treatment. Finally, with RNA-seq, we identified a set of genes, largely immune-related, induced by cytokine treatment. These gene expression profiles provide new insights into cytokine response of proximal tubule cells.

scholarly journals TWENTY-FOUR GENES ARE UPREGULATED IN PATIENTS WITH HYPOSPADIAS

2013 ◽  
Vol 16 (2) ◽  
pp. 39-43 ◽  
Author(s):  
R. Karabulut ◽  
Z. Turkyilmaz ◽  
K. Sonmez ◽  
G. Kumas ◽  
Sg. Ergun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Association Studies ◽  
Gene Expression Profiles ◽  
Ventral Surface ◽  
Genome Wide Association Studies ◽  
Expression Array ◽  
Large Patient ◽  
Expression Studies ◽  
Genome Wide

ABSTRACT Hypospadias is a congenital hypoplasia of the penis, with displacement of the urethral opening along the ventral surface, and has been reported to be one of the most common congenital anomalies, occurring in approximately 1:250 to 1:300 live births. As hypospadias is reported to be an easily diagnosed malformation at the crossroads of genetics and environment, it is important to study the genetic component in order to elucidate its etiology. In this study, the gene expression profiles both in human hypospadias tissues and normal penile tissues were studied by Human Gene Expression Array. Twentyfour genes were found to be upregulated. Among these, ATF3 and CYR61 have been reported previously. Other genes that have not been previously reported were also found to be upregulated: BTG2, CD69, CD9, DUSP1, EGR1, EIF4A1, FOS, FOSB, HBEGF, HNRNPUL1, IER2, JUN, JUNB, KLF2, NR4A1, NR4A2, PTGS2, RGS1, RTN4, SLC25A25, SOCS3 and ZFP36 (p <0.05). Further studies including genome-wide association studies (GWAS) with expression studies in a large patient group will help us for identifiying the candidate gene(s) in the etiology of hypospadias

Genome-wide gene expression profiles in response to plastid division perturbations

Planta ◽  
2011 ◽  
Vol 234 (5) ◽  
pp. 1055-1063 ◽  
Author(s):  
Jodi Maple ◽  
Per Winge ◽  
Astrid Elisabeth Tveitaskog ◽  
Daniela Gargano ◽  
Atle M. Bones ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Plastid Division ◽  
Genome Wide ◽  
Genome Wide Gene Expression
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