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Deep-sequencing influences the results obtained in small-RNA sequencing

ABSTRACT: This study presents a comparison of small RNA sequencing libraries generated from the same cell lines but using different sequencing platforms and protocols. The samples were analyzed and compared at the level of miRNAs expression and as a population of small RNAs derived from repetitive elements. Despite a good correlation between sequencing platforms, there are qualitative and quantitative variations in the results depending on the protocol used.

ORGANISM(S): Mus musculus

PROVIDER: GSE35368 | GEO | 2012/03/01

SECONDARY ACCESSION(S): PRJNA152595

REPOSITORIES: GEO

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Deep-sequencing influences the results obtained in small-RNA sequencing

Project description:This study presents a comparison of small RNA sequencing libraries generated from the same cell lines but using different sequencing platforms and protocols. The samples were analyzed and compared at the level of miRNAs expression and as a population of small RNAs derived from repetitive elements. Despite a good correlation between sequencing platforms, there are qualitative and quantitative variations in the results depending on the protocol used. 10 samples were examined: 6 from the ES E14 XY cell type: 1 454, 2 SOLiD from 2 technological versions, and 3 SOLEXA from 3 different protocols, and 4 samples from ES PGK XX cells: 1 454 and 1 SOLEXA sample, and 2 SOLiD samples from 2 technological versions.

2012-03-01 | E-GEOD-35368 | biostudies-arrayexpress

Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

Project description: Not available

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The Small RNA Profile of Silkworm Hemolymph Using Deep Sequencing

Project description:Human utilization of the mulberry-silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species (Morus notabilis C. K. Schneider). In the 330 Mb genome assembly of M. notabilis, we identified 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which were supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ~3 times faster than other Rosales, perhaps facilitating its spread to Europe, Africa, and America. It is among few eudicots but several Rosales not preserving genome duplications in more than 100 million years – however neopolyploid series in mulberry and several others suggest that new duplications may confer benefits. Strikingly, five predicted mulberry miRNAs were found in the hemolymph and silkglands of silkworm, suggesting profound molecular level interactions that promise to expand knowledge of plant-herbivore relationship which constitute key elements of most terrestrial habitats. In addition, we investigated the characters of hemolymph small RNA. small mRNA profiles of silkworm hemolymph in the fifth instar day-5 silkworm were generated by deep sequencing, in twice, using Illumina Hiseq 2000.

2013-09-12 | E-GEOD-48168 | biostudies-arrayexpress

Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (SOLiD)

2009-07-28 | E-GEOD-16370 | biostudies-arrayexpress

Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (454)

2009-07-28 | E-GEOD-16369 | biostudies-arrayexpress

Limitations and possibilities of small RNA digital gene expression profiling: spleen and liver comparison (SOLiD)

2009-07-28 | E-GEOD-16371 | biostudies-arrayexpress

Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNAs replicates (SOLiD)

2009-07-28 | E-GEOD-16372 | biostudies-arrayexpress

Limitations and possibilities of small RNA digital gene expression profiling

Project description:Analysis of RNA samples by massive parallel sequencing holds the promise to assay gene expression in both a quantitative and qualitative fashion and therefore allows for digital gene expression (DGE) profiling. We assessed the effect of different experimental approaches by generating small RNA libraries from a biological sample as well as an equimolar pool of synthetic miRNAs and analyzed the results using capillary dideoxy sequencing and next-generation sequencing platforms (Roche/454, AB/SOLiD and Illumina/Solexa). Whereas different sequencing platforms provided highly similar results, large differences in DGE profiles were observed depending on the library preparation method used. Nevertheless, our results indicate that the preferential nature of the library preparation methods is systematic and highly reproducible and we show that DGE is well suited for the quantification of relative expression differences between samples. This SuperSeries is composed of the following subset Series: GSE16369: Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (454) GSE16370: Limitations and possibilities of small RNA digital gene expression profiling: library preparation comparison (SOLiD) GSE16371: Limitations and possibilities of small RNA digital gene expression profiling: spleen and liver comparison (SOLiD) GSE16372: Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNAs replicates (SOLiD) GSE16373: Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNA replicates (Illumina) Refer to individual Series

2009-07-28 | E-GEOD-16374 | biostudies-arrayexpress

Limitations and possibilities of small RNA digital gene expression profiling: synthetic miRNA replicates (Illumina)

2009-07-28 | E-GEOD-16373 | biostudies-arrayexpress

RNA sequencing results of treatment with BET inhibitor (JQ1) in human diffuse large B-cell lymphoma (DLBCL) cells based on Illumina HiSeq 2500 platform

Project description:High-throughput RNA sequencing Analysis of human diffuse large B-cell lymphoma (DLBCL) cells treated with BET inhibitor. Our study represents the detailed analysis of the more accurate quantitative and qualitative evaluation of mRNA content within DBLBC cells. Our study represents the detailed analysis of the more accurate quantitative and qualitative evaluation of mRNA content within DLBCL cells.

2022-03-01 | GSE144821 | GEO

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