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identifier PRJDB1881
type bioproject
sameAs
sra-study  DRP001936
organism Homo sapiens
title Omics catalogue of lung adenocarcinoma cell lines
description Cancer cells carry various types of aberrations at the levels of genome, epigenome and transcriptome. For future studies on the biological relevance of the aberrations and their mutual relations, we generated a multi-omics catalogue of 26 lung adenocarcinoma cell lines. By whole-genome sequencing, we detected SNVs and indels, copy number aberrations and chromosome rearrangements. We used RNA-Seq to examine whether those mutation-harboring genes are expressed in the corresponding cell lines or whether their expression levels are deviated between the cell lines. Also, we could detect known and novel abnormal transcripts, such as RET- and ALK-fusion transcripts and transcripts caused by splice site mutations. Similarly, target-captured bisulfite sequencing and ChIP-Seq analyses revealed epigenomic status in each cell line and their deviations. We integrated these multi-omics data to explain possible causes of the observed aberrant gene expressions, particular for the representative cancer-related genes. We unexpectedly found that the patterns of aberrations were highly diverse between genes; namely irregular chromatin status revealed by ChIP-Seq was the characteristic to the EGFR, while a large genomic deletion and hyper-DNA methylation in the promoter region were the most frequent for the CDKN2A gene. Our datasets, by complementing current whole-exome or whole-genome sequencing of clinical cancers, should lay valuable base for interpreting how various types of genomic and epigenomic aberration lead to aberrant transcriptomic appearances in cancers.
data type Other
external link
properties 
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dbXrefs
sra-run  DRR016831DRR016832DRR016833DRR016834DRR016835DRR016836DRR016837DRR016838DRR016839DRR021359 More
sra-submission  DRA001858DRA002311
biosample  SAMD00003160SAMD00003161SAMD00003162SAMD00018550SAMD00018551SAMD00018552SAMD00018553SAMD00018554SAMD00018555SAMD00018556 More
sra-study  DRP002380DRP001936
sra-sample  DRS014677DRS014678DRS014679DRS016645DRS016646DRS016647DRS016648DRS016649DRS016650DRS016651 More
sra-experiment  DRX015184DRX015185DRX015186DRX015187DRX015188DRX015189DRX019512DRX019513DRX019514DRX019515 More
distribution JSONJSON-LD
status public
visibility unrestricted-access
dateCreated 2014-05-12T00:46:27+0000
dateModified 2015-02-06T08:23:46+0000
datePublished 2015-02-06T08:23:46+0000