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| Status |
Public on May 10, 2013 |
| Title |
A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females [Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Study of primary non-small cell lung adenocarcinoma tumors and normal tissues of 6 patients.
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| Contributor(s) |
Lee S, Kim J, Kim J, Lee J |
| Citation(s) |
23405175 |
| Submission date |
May 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sanghyuk Lee |
| E-mail(s) |
sanghyuk@ewha.ac.kr
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| Phone |
+82-42-879-8511
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| Fax |
+82-42-879-8519
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| URL |
http://www.kobic.re.kr
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| Organization name |
KRIBB
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| Department |
KOBIC
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| Street address |
125 Gwahak-ro
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| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (36)
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| GSM927308 |
Non-smoker female, NSCLC, RNA-seq [P1N] |
| GSM927309 |
Non-smoker female, NSCLC, RNA-seq [P1T] |
| GSM927310 |
Non-smoker female, NSCLC, RNA-seq [P3N] |
| GSM927311 |
Non-smoker female, NSCLC, RNA-seq [P3T] |
| GSM927312 |
Non-smoker female, NSCLC, RNA-seq [P4N] |
| GSM927313 |
Non-smoker female, NSCLC, RNA-seq [P4T] |
| GSM927314 |
Non-smoker female, NSCLC, RNA-seq [P5N] |
| GSM927315 |
Non-smoker female, NSCLC, RNA-seq [P5T] |
| GSM927316 |
Non-smoker female, NSCLC, RNA-seq [P6N] |
| GSM927317 |
Non-smoker female, NSCLC, RNA-seq [P6T] |
| GSM927318 |
Non-smoker female, NSCLC, RNA-seq [P8N] |
| GSM927319 |
Non-smoker female, NSCLC, RNA-seq [P8T] |
| GSM927320 |
Non-smoker female, NSCLC, smRNA-Seq [P1N] |
| GSM927321 |
Non-smoker female, NSCLC, smRNA-Seq [P1T] |
| GSM927322 |
Non-smoker female, NSCLC, smRNA-Seq [P3N] |
| GSM927323 |
Non-smoker female, NSCLC, smRNA-Seq [P3T] |
| GSM927324 |
Non-smoker female, NSCLC, smRNA-Seq [P4N] |
| GSM927325 |
Non-smoker female, NSCLC, smRNA-Seq [P4T] |
| GSM927326 |
Non-smoker female, NSCLC, smRNA-Seq [P5N] |
| GSM927327 |
Non-smoker female, NSCLC, smRNA-Seq [P5T] |
| GSM927328 |
Non-smoker female, NSCLC, smRNA-Seq [P6N] |
| GSM927329 |
Non-smoker female, NSCLC, smRNA-Seq [P6T] |
| GSM927330 |
Non-smoker female, NSCLC, smRNA-Seq [P8N] |
| GSM927331 |
Non-smoker female, NSCLC, smRNA-Seq [P8T] |
| GSM927338 |
Non-smoker female, NSCLC, MeDIP-Seq [P1N] |
| GSM927339 |
Non-smoker female, NSCLC, MeDIP-Seq [P1T] |
| GSM927340 |
Non-smoker female, NSCLC, MeDIP-Seq [P3N] |
| GSM927341 |
Non-smoker female, NSCLC, MeDIP-Seq [P3T] |
| GSM927342 |
Non-smoker female, NSCLC, MeDIP-Seq [P4N] |
| GSM927343 |
Non-smoker female, NSCLC, MeDIP-Seq [P4T] |
| GSM927344 |
Non-smoker female, NSCLC, MeDIP-Seq [P5N] |
| GSM927345 |
Non-smoker female, NSCLC, MeDIP-Seq [P5T] |
| GSM927346 |
Non-smoker female, NSCLC, MeDIP-Seq [P6N] |
| GSM927347 |
Non-smoker female, NSCLC, MeDIP-Seq [P6T] |
| GSM927348 |
Non-smoker female, NSCLC, MeDIP-Seq [P8N] |
| GSM927349 |
Non-smoker female, NSCLC, MeDIP-Seq [P8T] |
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| This SubSeries is part of SuperSeries: |
| GSE37765 |
A high dimensional deep sequencing study of non-small cell lung adenocarcinoma in never-smoker Korean females |
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| Relations |
| BioProject |
PRJNA163279 |
| SRA |
SRP012656 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE37764_RAW.tar |
215.3 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE37764_mRNA_NEUMA_gFVKM.xlsx.gz |
2.6 Mb |
(ftp)(http) |
XLSX |
| GSE37764_mRNA_NEUMA_iFVKM.xlsx.gz |
4.2 Mb |
(ftp)(http) |
XLSX |
| GSE37764_mRNA_P1.NEUMA_gFVKM.txt.gz |
259.4 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P1.NEUMA_iFVKM.txt.gz |
491.2 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P3.NEUMA_gFVKM.txt.gz |
259.5 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P3.NEUMA_iFVKM.txt.gz |
491.3 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P4.NEUMA_gFVKM.txt.gz |
258.7 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P4.NEUMA_iFVKM.txt.gz |
488.8 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P5.NEUMA_gFVKM.txt.gz |
258.1 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P5.NEUMA_iFVKM.txt.gz |
488.3 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P6.NEUMA_gFVKM.txt.gz |
258.3 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P6.NEUMA_iFVKM.txt.gz |
488.6 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P8.NEUMA_gFVKM.txt.gz |
256.8 Kb |
(ftp)(http) |
TXT |
| GSE37764_mRNA_P8.NEUMA_iFVKM.txt.gz |
480.9 Kb |
(ftp)(http) |
TXT |
| GSE37764_smRNA_P1.TMM.txt.gz |
6.8 Kb |
(ftp)(http) |
TXT |
| GSE37764_smRNA_P3.TMM.txt.gz |
6.7 Kb |
(ftp)(http) |
TXT |
| GSE37764_smRNA_P4.TMM.txt.gz |
6.7 Kb |
(ftp)(http) |
TXT |
| GSE37764_smRNA_P5.TMM.txt.gz |
6.7 Kb |
(ftp)(http) |
TXT |
| GSE37764_smRNA_P6.TMM.txt.gz |
6.8 Kb |
(ftp)(http) |
TXT |
| GSE37764_smRNA_P8.TMM.txt.gz |
6.7 Kb |
(ftp)(http) |
TXT |
| GSE37764_smallRNA_TMM.xlsx.gz |
293.9 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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