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identifier PRJDB2256
type bioproject
sameAs
sra-study  DRP001919
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  DRR016694DRR016695DRR016696DRR016697DRR016698DRR016699DRR016700DRR016701DRR016702DRR016703 More
sra-submission  DRA001846
biosample  SAMD00009596SAMD00009600SAMD00009578SAMD00009593SAMD00009599SAMD00009583SAMD00009598SAMD00009587SAMD00009588SAMD00009590 More
sra-study  DRP001919
sra-sample  DRS014543DRS014544DRS014545DRS014546DRS014547DRS014548DRS014549DRS014550DRS014551DRS014552 More
sra-experiment  DRX015047DRX015048DRX015049DRX015050DRX015051DRX015052DRX015053DRX015054DRX015055DRX015056 More
distribution JSONJSON-LD
status public
visibility unrestricted-access
dateCreated 2014-05-12T00:46:27+0000
dateModified 2015-02-06T08:21:34+0000
datePublished 2015-02-06T08:21:34+0000