Large-Scale Transcriptome Analysis

Weaver, David A.; Gopalakrishnan, Kathirvel; Joe, Bina

doi:10.1007/978-1-4939-6625-7_1

Cited by 3 publications

(3 citation statements)

References 10 publications

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“…RNA profiles can be easily obtained with global analysis of the isolated and purified total RNAs from tissues and body fluids with RNA‐seq (Chowdhury et al, 2020; Weaver et al, 2017). A large number of messenger RNAs (mRNAs) and ncRNAs were commonly identified as key components to regulate cancer‐signaling pathways (Yang et al, 2014).…”

Section: Current Status Of Multiomics Studies Of Pasmentioning

confidence: 99%

The use of mass spectrometry in a proteome‐centered multiomics study of human pituitary adenomas

Desiderio

Zhan

2021

Mass Spectrometry Reviews

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A pituitary adenoma (PA) is a common intracranial neoplasm, and is a complex, chronic, and whole-body disease with multicausing factors, multiprocesses, and multiconsequences. It is very difficult to clarify molecular mechanism and treat PAs from the single-factor strategy model. The rapid development of multiomics and systems biology changed the paradigms from a traditional single-factor strategy to a multiparameter systematic strategy for effective management of PAs.A series of molecular alterations at the genome, transcriptome, proteome, peptidome, metabolome, and radiome levels are involved in pituitary tumorigenesis, and mutually associate into a complex molecular network system. Also, the center of multiomics is moving from structural genomics to phenomics, including proteomics and metabolomics in the medical sciences. Mass spectrometry (MS) has been extensively used in phenomics studies of human PAs to clarify molecular mechanisms, and to discover biomarkers and therapeutic targets/drugs. MS-based

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Section: Current Status Of Multiomics Studies Of Pasmentioning

confidence: 99%

The use of mass spectrometry in a proteome‐centered multiomics study of human pituitary adenomas

Desiderio

Zhan

2021

Mass Spectrometry Reviews

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“…Three MR219 and three OsABP57 transgenic rice samples of control and treated were harvested and RNA extraction from leaves was performed according to TRIzol reagent (Life Technologies, Carlsbad, CA, USA) and purified using ethanol precipitation method [14]. Genomic DNA was lysed using TURBO DNase Kit (Ambion, Austin, TX, USA).…”

Section: Rna Extraction and Semi-quantitative Polymerase Chain Reaction (Pcr)mentioning

confidence: 99%

Effect of Rice AUXIN BINDING PROTEIN57 (OsABP57) Overexpression in Response to Flooding

Zambrose¹,

Roszelin²,

Hazbir³

et al. 2020

JAST-B

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This study reports the effects of Oryza sativa AUXIN BINDING PROTEIN57 (OsABP57) overexpression towards flooding in rice. OsABP57 was previously reported to activate plasma membrane H + -ATPase. Earlier studies address the ability of transgenic OsABP57 overexpression in enduring drought and salinity stresses but none on the flooding. In this study, complete submergence analysis was carried out and several morphophysiological parameters were analyzed such as plant height, root architecture and relative chlorophyll content. Results showed that there are no differences between OsABP57 overexpression rice compared to MR219 control rice in terms of chlorophyll content and plant height after 1-3 weeks of flooding treatments. Root analysis, however, found that transgenic rice OsABP57 produced more adventitious roots compared to MR219 rice under normal condition, which may be due to the role of the gene that encodes for auxin binding protein. The semi-quantitative polymerase chain reaction (PCR) on Oryza sativa pyruvate decarboxylase (OsPDC) gene after two weeks of flooding treatment showed an increase of expression in OsABP57 transgenic compared to MR219. Overall, the overexpression of OsABP57 did not show any significant difference in terms of morphophysiological analysis between the transgenic line and MR219, yet, there is an increase of OsPDC gene in the transgenic background which may need further experimental analysis in the future to map the network between auxin and hypoxia core genes.

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“…Leaves from the control, PEG-, and NaCl-treated group were sampled 3 hr after treatment in a triplicate biological control. The total RNA was extracted using a TRIzol reagent (Life Technologies) and was purified using the ethanol precipitation method (Weaver et al, 2017). Genomic DNA was discarded using the TURBO DNase Kit (Ambion) and first-strand cDNA was synthesised using the First Strand cDNA Synthesis Kit (Maxima).…”

Section: Isolation Of Total Rna From Kuku Belangmentioning

confidence: 99%

Molecular characterization of OsCURT1A from upland rice in response to osmotic stress

et al. 2019

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CURT1 proteins in Arabidopsis thaliana have been reported to be important for inducing grana curvature. Currently, we have identified transcript encoding CURT1A from Oryza sativa cv. indica through RNA-seq analysis and characterised using heterologous system in Arabidopsis. The OsCURT1A gene shares 80% of its amino acid sequence with Arabidopsis AtCURT1A. Phylogenetic analysis revealed that the OsCURT1A is also closely related to the CURT1 proteins in other choloroplast- conatining organisms. In silico analysis of OsCURT1A promoter shows that several cis-elements related to stress are present in the 5' upstream from the coding region. Under normal conditions, there were no notable changes in the phenotype and chlorophyll a;b ratio between three Arabidopsis genotypes, which were overexpressed (35S::OsCURT1A), T-DNA insertional mutant line (atcurt1a), and Wild type (Col-0). However, overexpression of OsCURT1A under salinity condition demonstrate high chlorophyll a:b compared to Col-0, whereas, the lack of atcurt1a gene in the mutant line showed reduced chlorophyll a:b ratio. These results indicate that the OsCURT1A might have a function as salt-stress related gene, which may indirectly regulate the chlorophyll a:b ratio. Therefore, OsCURT1A can be used as a potential candidate for salinity stress tolerance in crop improvement.

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Large-Scale Transcriptome Analysis

Cited by 3 publications

References 10 publications

The use of mass spectrometry in a proteome‐centered multiomics study of human pituitary adenomas

The use of mass spectrometry in a proteome‐centered multiomics study of human pituitary adenomas

Effect of Rice AUXIN BINDING PROTEIN57 (OsABP57) Overexpression in Response to Flooding

Molecular characterization of OsCURT1A from upland rice in response to osmotic stress

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