RNA-Seq-Based Transcriptomic Analysis of Saccharopolyspora spinosa Revealed the Critical Function of PEP Phosphonomutase in the Replenishment Pathway

2020 ◽  
Vol 68 (49) ◽  
pp. 14660-14669
Author(s):  
Zhudong Liu ◽  
Zirong Zhu ◽  
Jianli Tang ◽  
Haocheng He ◽  
Qianqian Wan ◽  
...  
Keyword(s):  
Transcriptomic Analysis ◽  
Rna Seq ◽  
Saccharopolyspora Spinosa ◽  
Critical Function

scholarly journals The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Xueyi Dong ◽  
Luyi Tian ◽  
Quentin Gouil ◽  
Hasaru Kariyawasam ◽  
Shian Su ◽  
...  
Keyword(s):  
Differential Expression ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Transcriptomic Analysis ◽  
Statistical Testing ◽  
Rna Seq ◽  
Sequencing Data ◽  
Short Read ◽  
Sequencing Platform ◽  
Long Read

Abstract Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity. However, such analysis can be challenging due to the high sequence error and small library sizes, which decreases quantification accuracy and reduces power for statistical testing. Here, we report the analysis of two nanopore RNA-seq datasets with the goal of obtaining gene- and isoform-level differential expression information. A dataset of synthetic, spliced, spike-in RNAs (‘sequins’) as well as a mouse neural stem cell dataset from samples with a null mutation of the epigenetic regulator Smchd1 was analysed using a mix of long-read specific tools for preprocessing together with established short-read RNA-seq methods for downstream analysis. We used limma-voom to perform differential gene expression analysis, and the novel FLAMES pipeline to perform isoform identification and quantification, followed by DRIMSeq and limma-diffSplice (with stageR) to perform differential transcript usage analysis. We compared results from the sequins dataset to the ground truth, and results of the mouse dataset to a previous short-read study on equivalent samples. Overall, our work shows that transcriptomic analysis of long-read nanopore data using long-read specific preprocessing methods together with short-read differential expression methods and software that are already in wide use can yield meaningful results.

Transcriptomic analysis of Camellia oleifera in response to drought stress using high throughput RNA-seq

2017 ◽  
Vol 64 (5) ◽  
pp. 728-737 ◽  
Author(s):  
H. Yang ◽  
H. Y. Zhou ◽  
X. N. Yang ◽  
J. J. Zhan ◽  
H. Zhou ◽  
...  
Keyword(s):  
Drought Stress ◽  
High Throughput ◽  
Transcriptomic Analysis ◽  
Camellia Oleifera ◽  
Rna Seq

scholarly journals Mechanisms of colitis-accelerated colon carcinogenesis and its prevention with the combination of aspirin and curcumin: Transcriptomic analysis using RNA-seq

2017 ◽  
Vol 135 ◽  
pp. 22-34 ◽  
Author(s):  
Yue Guo ◽  
Zheng-Yuan Su ◽  
Chengyue Zhang ◽  
John M. Gaspar ◽  
Rui Wang ◽  
...  
Keyword(s):  
Colon Carcinogenesis ◽  
Transcriptomic Analysis ◽  
Rna Seq

RNA-Seq-mediated transcriptomic analysis of heat stress response in a polar Chlorella sp. (Trebouxiophyceae, Chlorophyta)

2018 ◽  
Vol 30 (6) ◽  
pp. 3103-3119 ◽  
Author(s):  
Sze-Wan Poong ◽  
Kok-Keong Lee ◽  
Phaik-Eem Lim ◽  
Tun-Wen Pai ◽  
Chiew-Yen Wong ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Transcriptomic Analysis ◽  
Rna Seq ◽  
Heat Stress Response ◽  
Chlorella Sp

scholarly journals Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts

2016 ◽  
Author(s):  
Vasilis Ntranos ◽  
Govinda M. Kamath ◽  
Jesse Zhang ◽  
Lior Pachter ◽  
David N. Tse
Keyword(s):  
Single Cell ◽  
Transcriptomic Analysis ◽  
Rna Seq ◽  
Standard Analysis ◽  
Novel Method ◽  
Computationally Intensive ◽  
Or Gene ◽  
Specific Modeling

Current approaches to single-cell transcriptomic analysis are computationally intensive and require assay-specific modeling which limit their scope and generality. We propose a novel method that departs from standard analysis pipelines, comparing and clustering cells based not on their transcript or gene quantifications but on their transcript-compatibility read counts. In re-analysis of two landmark yet disparate single-cell RNA-Seq datasets, we show that our method is up to two orders of magnitude faster than previous approaches, provides accurate and in some cases improved results, and is directly applicable to data from a wide variety of assays.

Transcriptomic analysis by RNA-seq of Escherichia coli O157:H7 response to prolonged cold stress

LWT ◽  
2018 ◽  
Vol 97 ◽  
pp. 17-24 ◽  
Author(s):  
Yaru Li ◽  
Donggen Zhou ◽  
Shuangfang Hu ◽  
Xinglong Xiao ◽  
Yigang Yu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cold Stress ◽  
Transcriptomic Analysis ◽  
Escherichia Coli O157 ◽  
Rna Seq

scholarly journals The landscape of gene fusions in hepatocellular carcinoma

2016 ◽  
Author(s):  
Chengpei Zhu ◽  
Yanling Lv ◽  
Liangcai Wu ◽  
Jinxia Guan ◽  
Xue Bai ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cancer Progression ◽  
Gene Fusion ◽  
Early Stage ◽  
Pcr Analysis ◽  
Gene Fusions ◽  
Fusion Genes ◽  
Rna Seq ◽  
Rt Pcr ◽  
Critical Function

AbstractMost hepatocellular carcinoma (HCC) patients are diagnosed at advanced stages and suffer limited treatment options. Challenges in early stage diagnosis may be due to the genetic complexity of HCC. Gene fusion plays a critical function in tumorigenesis and cancer progression in multiple cancers, yet the identities of fusion genes as potential diagnostic markers in HCC have not been investigated.Paired-end RNA sequencing was performed on noncancerous and cancerous lesions in two representative HBV-HCC patients. Potential fusion genes were identified by STAR-Fusion in STAR software and validated by four publicly available RNA-seq datasets. Fourteen pairs of frozen HBV-related HCC samples and adjacent non-tumor liver tissues were examined by RT-PCR analysis for gene fusion expression.We identified 2,354 different gene fusions in the two HBV-HCC patients. Validation analysis against the four RNA-seq datasets revealed only 1.8% (43/2,354) as recurrent fusions that were supported by public datasets. Comparison with four fusion databases demonstrated that three (HLA-DPB2-HLA-DRB1, CDH23-HLA-DPB1, and C15orf57-CBX3) out of 43 recurrent gene fusions were annotated as disease-related fusion events. Nineteen were novel recurrent fusions not previously annotated to diseases, including DCUN1D3-GSG1L and SERPINA5-SERPINA9. RT-PCR and Sanger sequencing of 14 pairs of HBV-related HCC samples confirmed expression of six of the new fusions, including RP11-476K15.1-CTD-2015H3.2.Our study provides new insights into gene fusions in HCC and could contribute to the development of anti-HCC therapy. RP11–476K15.1-CTD–2015H3.2 may serve as a new therapeutic biomarker in HCC.

Sign in / Sign up

Export Citation Format

Share Document