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Transcriptomic analysis by AmpliSeq Ion Torrent to explore the effects of the long non-coding RNA TGFB2-AS1 on gene expression in human keratinocytes

ABSTRACT: Transcriptomic analysis by AmpliSeq Ion Torrent to explore the effects of the long non-coding RNA TGFB2-AS1 on gene expression in human keratinocytes

PROVIDER: PRJEB31679 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3219190.fastq.gz	Fastqsanger.gz
	ERR3219191.fastq.gz	Fastqsanger.gz
	ERR3219192.fastq.gz	Fastqsanger.gz
	ERR3219193.fastq.gz	Fastqsanger.gz
	ERR3219194.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis by AmpliSeq Ion Torrent to explore the effects of the long non-coding RNA TGFB2-AS1 on gene expression in human keratinocytes

Project description:TGFB2-AS1 is a long non-coding RNA which is induced by ΤGFβ signaling. In order to assess the importance of TGFB2-AS1 on the regulation of gene expression, we performed an AmpliSeq transcriptomic array in human keratinocytes (HaCaT), which stably over-express TGFB2-AS1 or control pcDNA3 empty vector. In addition, cells were stimulated with TGFβ1 for 24 hours, in order to observe the effects of TGFB2-AS1 on gene expression, downstream of TGFβ signaling. RNA from the following four conditions was used in this experiment: 1) pcDNA3, 2) pcDNA3+TGFβ1, 3) pcDNA3-TGFB2-AS1, 4) pcDNA3-TGFB2-AS1+TGFβ1. Biological triplicates were used per condition.

2019-07-01 | E-MTAB-7773 | biostudies-arrayexpress

Transcriptomic analysis by AmpliSeq Ion Torrent to to understand the role of LKB1 and PARD3 in Glioblastoma biology

Project description:The aim of this work was to elucidate the role of LKB1/STK11 and PARD3 in glioblastoma multiforme cells. For this we silenced the expression of these proteins using specific siRNA in two different patient-derived glioblastoma stem cells, U3031MG and U3034MG, then we analysed how the knock-down of these genes affects gene expression using Ion torrent AmpliseqTM.

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Comprehensive Evaluation of AmpliSeq Transcriptome, a Novel Targeted Whole Transcriptome RNA Sequencing Methodology for Global Gene Expression Analysis.

Project description:Background: Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. The Ion AmpliSeqTM Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq.To assess the performance of this new methodology, we performed a comprehensive comparison of AmpliSeq with RNA-seq using two well-established next-generation sequencing platforms (Illumina HiSeq and Ion Torrent Proton). We analyzed standard reference RNA samples and RNA samples obtained from human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs). Results: Using published data from two standard RNA reference samples, we observed a strong concordance of log2 fold change for all genes when comparing AmpliSeq to Illumina HiSeq (Pearson’s r=0.92) and Ion Torrent Proton (Pearson’s r=0.92). We used ROC, Matthew’s correlation coefficient and RMSD to determine the overall performance characteristics. All three statistical methods demonstrate AmpliSeq as a highly accurate method for differential gene expression analysis. Additionally, for genes with high abundance, AmpliSeq outperforms the two RNA-seq methods. When analyzing four closely related hiPSC-CM lines, we show that both AmpliSeq and RNA-seq capture similar global gene expression patterns consistent with known sources of variations. Conclusions: Our study indicates that AmpliSeq excels in the limiting areas of RNA-seq for gene expression quantification analysis. Thus, AmpliSeq stands as a very sensitive and cost-effective approach for very large scale gene expression analysis and mRNA marker screening with high accuracy.

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Transcriptomic analysis by AmpliSeq Ion Torrent to to understand the role of LKB1 and PARD3 in Glioblastoma biology

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