Unknown,Transcriptomics,Genomics,Proteomics

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Transposon-based construction of strand-specific RNA-seq libraries

ABSTRACT: We have developed two methods for efficiently consructing RNA-seq libraries using transposition. Each method constructs high quality RNA-seq libraries when compared to standard approaches. One of the methods (Directional Tn-RNA-seq) maintains strand-of-origin information and exhibits strand specificity comparable to current approaches. RNA-seq libraries were constructed from ECC-1, a human cell line, and Universal Human Reference RNA using transposon-based and standard RNA-seq library construciton methods.

ORGANISM(S): Homo sapiens

SUBMITTER: Jason Gertz

PROVIDER: E-GEOD-32307 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transposase mediated construction of RNA-seq libraries.

Gertz Jason J Varley Katherine E KE Davis Nicholas S NS Baas Bradley J BJ Goryshin Igor Y IY Vaidyanathan Ramesh R Kuersten Scott S Myers Richard M RM

Genome research 20111129 1

RNA-seq has been widely adopted as a gene-expression measurement tool due to the detail, resolution, and sensitivity of transcript characterization that the technique provides. Here we present two transposon-based methods that efficiently construct high-quality RNA-seq libraries. We first describe a method that creates RNA-seq libraries for Illumina sequencing from double-stranded cDNA with only two enzymatic reactions. We generated high-quality RNA-seq libraries from as little as 10 pg of mRNA ...[more]

PMID: 22128135

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Project description:Endometrial cancer (EC) is the most common cancer of female reproductive organs. Because some low-grade ECs might also experience tumor recurrence after surgery and a worse prognosis, the study of alterations related to EC pathogenesis of the disease might help to get insights into underlying mechanisms involved in EC development and metastasis and identify novel markers associated to the disease. Here, low C1GALT1 protein expression levels were associated to a more aggressive phenotype of EC. Then, we aimed at investigating the role of C1GALT1 in EC progression by quantitative proteomics. ECC-1 cells were used as endometrioid EC model, and the effect of C1GALT1 depletion was analyzed using C1GALT1 specific short hairpin RNAs (shRNA) in comparison to SCRAMBLE shRNA. SILAC and mass spectrometry analysis were performed to identify and quantify dysregulated proteins associated with C1GALT1 depletion in the cell extract and secretome proteome of shC1GALT1 and SCRAMBLE ECC-1 cells. Out of 5208 proteins identified and quantified by LC-MS/MS, 76 and 143 proteins showed dysregulation (fold-change ≥1.5 or ≤0.67) in shC1GALT1 ECC-1 cells’ extracts and secretome, respectively. Nine dysregulated proteins were selected for validation by orthogonal techniques, confirming their dysregulation upon C1GALT1 depletion. Bioinformatics analyses pointed out to an increase in pathways and dysregulated proteins that associated with more aggressive phenotype. This finding was corroborated by loss-of-function cell-based assays. A higher proliferation, invasion, migration, colony formation and angiogenesis capacity of C1GALT1 depleted cells was observed. Finally, the negative protein expression correlation found by proteomics between C1GALT1 and LGALS3 was confirmed by IHC in actual EC samples, suggesting C1GALT1 stably depleted ECC-1 cells mimic the aggressive phenotype of EC cells and might be useful for the identification and validation of potential markers in aggressive ECs.

Dataset Information

Transposon-based construction of strand-specific RNA-seq libraries

Publications

Transposase mediated construction of RNA-seq libraries.

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