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| Status |
Public on Nov 30, 2019 |
| Title |
RNA-seq transcriptome analysis in NCI-H209 and NCI-H441 cells transfected with TTF-1/NKX2-1 or ASCL1 siRNAs. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Although Thyroid transcription factor-1 (TTF-1, encoded by NKX2-1 gene) is highly expressed in small cell lung carcinoma (SCLC) and lung adenocarcinoma (LADC), difference in the functional roles of TTF-1 between SCLC and LADC remains to be elucidated. The aim of this study was to clarify the differences in the TTF-1 binding regions and functional roles in SCLC and LADC. Employing chromatin immunoprecipitation-sequencing (ChIP-seq) , here we compared the genome-wide TTF-1-binding profiles and the TTF-1-mediated transcriptional programs in a SCLC and a LADC cell lines. We also investigated ASCL1 binding regions in SCLC cells. To validate whether the changes in TTF-1 or ASCL1 binding to the genome indeed resulted in changes in target gene expression, we performed RNA-seq transcriptome analyses in H209 cells with TTF-1 or ASCL1 knockdown. Data were also obtained from H441 cells transfected with TTF-1 siRNAs.
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| Overall design |
RNA-seq transcriptome analyses performed in a small cell lung carcinoma NCI-H209 cells with TTF-1 or ASCL1 knockdown. RNA-seq data were also obtained from a lung adenocarcinoma NCI-H441 cells transfected with TTF-1 siRNAs.
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| Contributor(s) |
Hokari S, Tamura Y, Morikawa M, Miyazono K, Koinuma D |
| Citation(s) |
31782890 |
| Submission date |
Apr 04, 2019 |
| Last update date |
Dec 01, 2019 |
| Contact name |
Daizo Koinuma |
| E-mail(s) |
d-koinuma@umin.ac.jp
|
| Organization name |
University of Tokyo
|
| Department |
Pathology
|
| Street address |
Hongo 7-3-1, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
| |
|
| Platforms (1) |
| GPL17303 |
Ion Torrent Proton (Homo sapiens) |
|
| Samples (9)
|
| GSM3711341 |
H209 treated with negative control siRNA (a control for ASCL1 depletion) |
| GSM3711342 |
H209 treated with ASCL1 siRNA #1 |
| GSM3711343 |
H209 treated with ASCL1 siRNA #2 |
| GSM3711344 |
H209 treated with negative control siRNA (a control for TTF-1 depletion) |
| GSM3711345 |
H209 treated with TTF-1 siRNA #1 |
| GSM3711346 |
H209 treated with TTF-1 siRNA #2 |
| GSM3711347 |
H441 treated with negative control siRNA |
| GSM3711348 |
H441 treated with TTF-1 siRNA #1 |
| GSM3711349 |
H441 treated with TTF-1 siRNA #2 |
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| This SubSeries is part of SuperSeries: |
| GSE129341 |
Comparative Analysis of TTF-1 Binding DNA Regions in Small Cell Lung Cancer and Non-Small Cell Lung Cancer |
|
| Relations |
| BioProject |
PRJNA530975 |
| SRA |
SRP190873 |
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