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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Sanghyuk Lee

PROVIDER: E-GEOD-37765 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers.

Kim Sang Cheol SC Jung Yeonjoo Y Park Jinah J Cho Sooyoung S Seo Chaehwa C Kim Jaesang J Kim Pora P Park Jehwan J Seo Jihae J Kim Jiwoong J Park Seongjin S Jang Insu I Kim Namshin N Yang Jin Ok JO Lee Byungwook B Rho Kyoohyoung K Jung Yeonhwa Y Keum Juhee J Lee Jinseon J Han Jungho J Kang Sangeun S Bae Sujin S Choi So-Jung SJ Kim Sujin S Lee Jong-Eun JE Kim Wankyu W Kim Jhingook J Lee Sanghyuk S

PloS one 20130206 2

<h4>Background</h4>Deep sequencing techniques provide a remarkable opportunity for comprehensive understanding of tumorigenesis at the molecular level. As omics studies become popular, integrative approaches need to be developed to move from a simple cataloguing of mutations and changes in gene expression to dissecting the molecular nature of carcinogenesis at the systemic level and understanding the complex networks that lead to cancer development.<h4>Results</h4>Here, we describe a high-throug ...[more]

PMID: 23405175

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A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females [aCGH]

Project description:One of the most fertile applications of next generation sequencing will be in the field of cancer genomics. Here, we report a high-throughput multi-dimensional sequencing study of primary non-small cell lung adenocarcinoma tumors and adjacent normal tissues of 6 never-smoker Korean female patients. Our data encompass results from exome-seq, RNA-seq, small RNA-seq, and MeDIP-seq. We identified and validated novel genetic aberrations including 47 somatic mutations and 20 fusion transcripts. We also characterized gene expression profiles which we sought to integrate with genomic aberrations and epigenetic regulations into functional networks. Importantly, among others the gene network module governing G2/M cell check point emerged as the primary source of disturbance in these patients. In addition, our study strongly suggests that microRNAs make key regulatory inputs into this gene network module. Our study offers a paradigm for integrative genomics analysis and proposes potential target pathways for the control of non-small cell lung adenocarcinoma. Study of primary non-small cell lung adenocarcinoma tumors and normal tissues of 6 patients.

2013-05-10 | E-GEOD-37759 | biostudies-arrayexpress

A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females [Seq]

2013-05-10 | E-GEOD-37764 | biostudies-arrayexpress

Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-07-03 | E-GEOD-58023 | biostudies-arrayexpress

Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [RNA-seq_differentiation]

Project description:Polycomb group (PcG) proteins are required for normal differentiation and development, and their activity is found deregulated in cancer. PcG proteins are involved in gene silencing, however, whether they initiate or maintain transcriptional repression is a subject of debate. Here, we show that knockout of the Polycomb repressive complex 2 (PRC2) does not lead to significant gene expression changes in mouse embryonic stem cells (mESCs), and that it is dispensable for initiating silencing of target genes during differentiation. Transcriptional inhibition in mESCs is sufficient to induce genome-wide ectopic PRC2 recruitment to endogenous PcG target genes found in other tissues. PRC2 binding analysis shows that it is restricted to nucleosome-free CpG islands (CGIs) of un-transcribed genes. Our results show that it is the transcriptional state that governs PRC2 binding, and we propose that it binds by default to non-transcribed CGI genes to maintain their silenced state and to protect cell identity. RNA-seq time-course experiments during in vitro differentiation (0h, 24h, 48h and 72h) of Mus musculus wild-type E14 and Suz12 knock-out Embryonic Stem Cells with two biological replicates per condition.

2014-07-03 | E-GEOD-58017 | biostudies-arrayexpress

ChAP-chip analysis of RpoA binding profiles on the B. subtilis chromosome in the intact and the C-terminal truncated RNAP alpha subunit expressing cells.

Project description:We constructed the B. subtilis strains in which the expression of the intact and the C-terminal truncated RNAP alpha subunit were induced by different stimulus, IPTG and xylose, under the control of Pspac and Pxyl promoters. Then, we performed ChAP-chip analysis to analyze the impact of alpha-CTD defect on genome-wide transcriptome profile.

2015-06-25 | E-MTAB-3385 | biostudies-arrayexpress

Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [iTC-seq_drugs]

Project description:Polycomb group (PcG) proteins are required for normal differentiation and development, and their activity is found deregulated in cancer. PcG proteins are involved in gene silencing, however, whether they initiate or maintain transcriptional repression is a subject of debate. Here, we show that knockout of the Polycomb repressive complex 2 (PRC2) does not lead to significant gene expression changes in mouse embryonic stem cells (mESCs), and that it is dispensable for initiating silencing of target genes during differentiation. Transcriptional inhibition in mESCs is sufficient to induce genome-wide ectopic PRC2 recruitment to endogenous PcG target genes found in other tissues. PRC2 binding analysis shows that it is restricted to nucleosome-free CpG islands (CGIs) of un-transcribed genes. Our results show that it is the transcriptional state that governs PRC2 binding, and we propose that it binds by default to non-transcribed CGI genes to maintain their silenced state and to protect cell identity. in vivo Trancription Capture-sequencing (iTC-seq) time-course experiments during transcriptional inhibition with either DRB (0h, 2h and 5h) or Triptolide (0h, 1h and 2h) treatment of Mus musculus wild-type E14 Embryonic Stem Cells with two biological replicates per condition.

2014-07-03 | E-GEOD-58018 | biostudies-arrayexpress

ChAP-chip analysis of RpoC binding profiles on the B. subtilis chromosome in the intact and the C-terminal truncated RNAP alpha subunit expressing cells.

Project description:We constructed the B. subtilis strains in which the expression of the intact and the C-terminal truncated RNAP alpha subunit were induced by different stimulus, IPTG and xylose, under the control of Pspac and Pxyl promoters. Then, we performed ChAP-chip analysis to analyze the impact of M-^UM-^AM-A-CTD defect on genome-wide transcriptome profile.

2015-06-25 | E-MTAB-3384 | biostudies-arrayexpress

Classification of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach

Project description:DNA methylation plays a significant role in assuring cell identity, thus potentiating its application in molecular classification of cancers in respect of tissue origins or clinically and aetiologically distinct subtypes. In this study, we adapted our liquid hybridization capture-based bisulfite sequencing approach on the targeted sequencing of promoter methylomes. We detected ten cell lines originated from different tissue origins and demonstrated a similar potentiality of promoter methylomes as classifiers for cancer cell lines from different tissue origins in comparison with gene expression profiles. Furthermore, promoter methylome can sensitively differentiate two different cell lines from the same tissue origin in respect of the CpG island methylator phenotype (CIMP), as in the case of AGS and BGC-823 gastric cancer cell lines. These results potentiate the targeted sequencing of promoter methylomes as a means for comprehensive screening and classifying cancer cells with respect to tissue-origins and CIMP subtypes in the future studies. We proved the potentiality of promoter-targeted LHC-BS that requires reduced experimental cost and less amount of initial DNA samples in comparison with a previous design [23] using YH cell line. In addition, we generated single-base promoter methylomes for ten cell lines, including eight cancer cell lines generated from four types of tissues and one pair of model cell lines for ovarian cancer (T29 and T29H). We proved the potentiality of promoter-targeted LHC-BS that requires reduced experimental cost and less amount of initial DNA samples in comparison with a previous design using YH cell line. In addition, we generated single-base promoter methylomes for ten cell lines, including eight cancer cell lines generated from four types of tissues and one pair of model cell lines for ovarian cancer (T29 and T29H).

2014-02-19 | E-GEOD-44866 | biostudies-arrayexpress

Transcription profiling of Staphylococcus aureus treated with tigecycline to determine the effect of the expression of virulence factors in biofilm-associated cells

Project description:Data is also available from <ahref=http://bugs.sgul.ac.uk/E-BUGS-81 target=_blank>BuG@Sbase</a>

2009-11-25 | E-BUGS-81 | biostudies-arrayexpress

ArrayCGH of human hepatocellular carcinoma (HCC)

Project description:We used array-based comparative genomic hybridization (arrayCGH) of 76 hepatocellular carcinomas (HCCs) to search for genetically disrupted genes. Seventy-six HCC clinical specimens were analyzed. Genomic DNA of the tumor sample was labeled with Cy5 and reference normal DNA (Promega) was labeled with Cy3.

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