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Series GSE39998 Query DataSets for GSE39998
Status Public on Jan 22, 2013
Title NKX2-1 occupancy in human lung adenocarcinoma cell lines
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The NKX2-1 transcription factor, a regulator of normal lung development, is the most significantly amplified gene in human lung adenocarcinoma. To better understand how genomic alterations of NKX2-1 drive tumorigenesis, we generated an expression signature associated with NKX2-1 amplification in human lung adenocarcinoma, and analyzed DNA binding sites of NKX2-1 by genome-wide chromatin immunoprecipitation from NKX2-1-amplified human lung adenocarcinoma cell lines. Combining these expression and cistromic analyses identified LMO3, itself encoding a transcription regulator, as a candidate direct transcriptional target of NKX2-1, in addition to consensus binding motifs including a nuclear hormone receptor signature and a Forkhead box motif in NKX2-1-bound sequences. RNA interference analysis of NKX2-1-amplified cells compared to non-amplified cells demonstrated that LMO3 mediates cell proliferation downstream of NKX2-1; cistromic analysis that NKX2-1 may cooperate with FOXA1. Our findings provide new insight into the transcriptional regulatory network of NKX2-1 and suggest that LMO3 is a transducer of lineage specific cell survival of NKX2-1-amplified lung adenocarcinomas.
Overall design NKX2-1 ChIP-seq from three lung adenocarcinoma cell lines with amplification of NKX2-1
Contributor(s) Watanabe H
Citation(s) 23322301
Submission date Aug 08, 2012
Last update date May 15, 2019
Contact name Hideo Watanabe
Organization name Icahn School of Medicine at Mount Sinai
Department Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine
Lab Hideo Watanabe
Street address One Gustave L. Levy Place
City New York
State/province NY
ZIP/Postal code 10029
Country USA
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (9)
GSM983097 H3122_input
GSM983098 H3122_NKX2-1_BL4000
GSM983099 H1819_input
BioProject PRJNA172254
SRA SRP014763

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Supplementary file Size Download File type/resource
GSE39998_RAW.tar 1.8 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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