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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type 、 ryhB-1、 ryhB-2、 ryhB-1/ryhB-2 Mutant Strains Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type 、 ryhB-1、 ryhB-2、 ryhB-1/ryhB-2 Mutant Strains Transcriptomes

PROVIDER: PRJNA828446 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type 、 ryhB-1、 ryhB-2、 ryhB-1/ryhB-2 Mutant Strains Transcriptomes

Project description:Purpose:To investigate the effect of small RNA RyhB-1and RyhB-2 deletion of Salmonella enteritidis on genes expression of genome under simulated intestinal conditions Methods:S. Enteritidis wild type (WT) strain 50336 and mutants △ryhB-1, △ryhB-2, and △ryhB-1/ryhB-2 were grown overnight in 50 mL of the LB medium with 160 rpm shaking at 37°C under aerobic condition, washed thrice, and re-suspended with iron-limited and nutrient-limited medium. The above prepared bacterial cells were cultured for 2 h at 37°C in the anaerobic workstation. Each sample was analysed in triplicate. Total RNA of the above stains was extracted using TRIzol reagentwith DNase digestion according to the manufacturer’s instruction. Ribosome RNA was removed using a Ribo-Zero rRNA removal kit (Illumina) that leaves the mRNA. Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), sequenced on an Illumina Hiseq 2000 platform at Beijing Novogene Bioinformatics Technology。 Results: Analysis of the RNA-Seq data identified 496, 250, and 553 DEGs in △ryhB-1, △ryhB-2, and △ryhB-1△ryhB-2, respectively, compared to the WT strain.A total of 213 genes changed in △ryhB-1, △ryhB-2, and △ryhB-1△ryhB-2 mutants. The transcriptional levels of 176 genes changed in △ryhB-1 and △ryhB-1△ryhB-2 but not in △ryhB-2. Furthermore, 14 genes were only changed in RyhB-2, 96 DEGs were only identified in △ryhB-1, and 12 DEGs were only identified in △ryhB-2 but not in △ryhB-1△ryhB-2. Moreover, 150 DEGs were only identified in △ryhB-1△ryhB-2 but neither in △ryhB-1 nor in △ryhB-2. Conclusions: A total of 213 genes could be regulated by △ryhB-1, △ryhB-2, and △ryhB-1△ryhB-2 mutants, 176 genes are regulated only by RyhB-1, 14 genes were regulated only by RyhB-2.

2022-04-23 | GSE201112 | GEO

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Project description: Not available

| S-EPMC3233386 | biostudies-literature

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and fl4 mutant Transcriptomes

Project description:Analysis of gene expression level. The hypothesis tested in the present study was that fl4 mutant influence the ER stress pathway. Results provide important information of the gene expression level regulation of different ER stress pathways and apoptosis Endosperm mRNA profiles of 19DAP wild type (WT) and fl4 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2000 (Zea mays).

2014-01-18 | E-GEOD-54184 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and pro1 mutant Transcriptomes

Project description:Analysis of gene expression level. The hypothesis tested in the present study was that pro1 mutant influence the cell cycle pathway. Results provide important information of the cell cycle-related gene expression level regulation of cell cycle transition from G1 to S phase. Seedling mRNA profiles of 14DAG wild type (WT) and pro1 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2000 (Zea mays).

2015-03-31 | E-GEOD-56004 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and opaque2 mutant Transcriptomes

Project description:Analysis of gene expression level. The hypothesis tested in the present study was that opaque2 mutant influence the expression of storage proteins. Results provide important information of the gene expression level regulation of storage proteins and other biological processes. Endosperm mRNA profiles of 15DAP wild type (WT) and opaque2 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

2014-10-15 | E-GEOD-61830 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and rea1 mutant Transcriptomes

Project description:Analysis of gene expression level. The hypothesis tested in the present study was that rea1 mutant influence the expression of translation and nucleosome assembly associated genes. Results provide important information of the gene expression level regulation of ribosome proteins, elongation factors, histones and genes associated with other biological processes. Endosperm mRNA profiles of 15DAP wild type (WT) and rea1 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

2015-04-25 | E-GEOD-67080 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and dek35 mutant Transcriptomes

Project description:Analysis of gene expression level. The hypothesis tested in the present study was that dek35 mutant influence the expression of mitochondrial oxidative phosphorylation associated genes. Results provide important information of the gene expression level regulation of mitochondrial complexes assembly proteins, translational elongation factors and genes associated with other biological processes. Endosperm mRNA profiles of 18DAP wild type (WT) and dek35 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

2016-03-25 | E-GEOD-79583 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

2021-02-27 | GSE164382 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ZmMADS47 RNAi mutant Transcriptomes

Project description:Analysis of gene expression level. The hypothesis tested in the present study was that ZmMADS47 RNAi mutant influence the expression of nutritional metabolism genes. Results provide important information of the gene expression level regulation of zein family. Maize kernel mRNA profiles of 15DAP wild type (WT) and ZmMADS47 RNAi mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2000 (Zea mays).

2015-07-10 | E-GEOD-70609 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Normal Human Kidney Transcriptomes

Project description:Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived normal human kidney transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis The kidney tissue was immediately placed and stored in RNAlater® (Ambion), according to the manufacturer’s instruction. The tissue was manually microdissected under microscope in RNAlater® pool for glomerular and tubular compartment. Dissected tissue was homogenized and RNA was prepared using RNAeasy mini columns (Qiagen, Valencia, CA, US), according to the manufacturer’s instructions. RNA quality and quantity were determined using the Laboratory-on-Chip Total RNA PicoKit Agilent BioAnalyzer. Only samples without evidence of degradation were further used (RNA Integrity Number >6).

2014-08-06 | E-GEOD-60119 | biostudies-arrayexpress

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