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High-throughput sequencing of WT and the yqhC mutant of Salmonella using Illumina Genome Analyzer II

ABSTRACT: Total RNA was isolated from WT and the mutant and the ribosomal RNA was removed using Ambion Kit. Construction of cDNA library, addition of adapters and sequence read were performed.

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium

PROVIDER: GSE24263 | GEO | 2011/09/29

SECONDARY ACCESSION(S): PRJNA132991

REPOSITORIES: GEO

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High-throughput sequencing of WT and the yqhC mutant of Salmonella using Illumina Genome Analyzer II

Project description:Total RNA was isolated from WT and the mutant and the ribosomal RNA was removed using Ambion Kit. Construction of cDNA library, addition of adapters and sequence read were performed. 2 samples were used, WT Salmonella and its yqhC mutant

2011-09-29 | E-GEOD-24263 | biostudies-arrayexpress

Comparison of mRNA-seq quantification from libraries obtained using either HD or standard Illumina adapters in A thaliana, in wildtype and DCL1 mutants

Project description:One method of directional cloning of fragmented mRNA is based on single strand RNA ligation, for which ligation bias occurrs if the adapters have single sequences. The sequencing bias affects the mRNA quantification and subsequently the differential expression analysis. High definition (HD) adapters [Sorefan et al 2012, Xu et al 2015] can be used to diminish the cloning bias during library construction. HD adapters and standard illumina adapters were used to construct mRNA-seq libraries for a side by side comparison.

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Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems.

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Project description:Total RNA was isolated from mouse lung harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA-Seq Kit (KAPA) and were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

2019-10-24 | GSE122492 | GEO

Transcriptomics analysis of gene expression in wildtype and NSUN2 knockdown T24 cell

Project description:Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-Seq library construction. RNA-Seq libraries was directly constructed by using KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length. The different genes expression between the control and NSUN2 knockdown cell were detected.

2019-07-02 | GSE133621 | GEO

Variant identification in multi-sample pools by illumina genome analyzer sequencing.

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High-throughput single-microparticle imaging flow analyzer.

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The Root-Knot Nematode Effector MiEFF18 Targets the Core Spliceosomal Protein SmD1 and Facilitates Giant Cell Formation

Project description:The goals of this study is understand the effect of the MiEFF18 nematode effector on alternative splicing. Methods: PolyA RNA from WT, MiEFF18 overexpressor and smd1b mutant seedlings were sequenced using the illumina NextSeq500 sequencer, in triplicate. Total RNA was extracted from the roots of the three Arabidopsis lines (Col0, OE-MiEFF18#13.6 and smd1b) with TriZol (Invitrogen), according to the Invitrogen protocol. The RNA was treated with DNAse treatment (Ambion), and its quality and integrity were assessed with a Bioanalyzer (Agilent). Libraries were constructed with the Tru-Seq Stranded mRNA Sample Prep kit (Illumina®). Paired-end sequencing with 75-bp reads was performed on a NextSeq500 perform. A minimum of 30 million paired-end reads per sample was generated. RNA-seq preprocessing included the trimming of library adapters and quality controls with Trimmomatic. Paired-end reads with a Phred Quality Score Qscore > 20 and a read length > 30 bases were retained, and ribosomal RNA sequences were removed with SortMeRNA. Processed reads were aligned using Tophat2 with the following arguments: --max-multihits 1 -i 20 --min-segment-intron 20 --min-coverage-intron 20 --library-type fr-firststrand --microexon-search -I 1000 --max-segment-intron 1000 --max-coverage-intron 1000 --b2-very-sensitive. Conclusions: MiEFF18 overexpression modifies the expression of genes important for the ontogenesis of giant cells, notably those involved in microtubule cytoskeleton reorganization and cell cycle regulation, strongly suggesting that MiEFF18-mediated SmD1 inactivation in plants leads to a loss of susceptibility to root-knot nematodes.

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Transcriptomics analysis of gene expression in human urothelial carcinoma of the bladder (UCB) and adjacent normal tissues.

Project description:36 cases of UCB and 29 adjacent normal bladder tissues (22 pairs) were derived from patients diagnosed with UCB and received radial cystectomy at Sun Yat-sen University Cancer Center (SYSUCC, Guangzhou, China). Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-Seq library construction. RNA-Seq libraries was directly constructed by using KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length. The different genes expression between the UCB and adjacent normal tissues were detected. Several genes related to cancer pathways were dysregulated.

2019-07-02 | GSE133624 | GEO

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