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| Status |
Public on Jul 27, 2014 |
| Title |
input DNA, A549 cells |
| Sample type |
SRA |
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| Source name |
A549_input
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| Organism |
Homo sapiens |
| Characteristics |
ttf-1 expression: negative
cell line: A549
histology: lung adenocarcinoma
chip antibody: none
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| Treatment protocol |
Cells were treated with 1 ng/ml of TGF-beta3 for 1.5 h.
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| Growth protocol |
A549 cells were maintained in Dulbecco's modified Eagle's medium (DMEM #11965; Life Technologies) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin G, and 100 µg/ml streptomycin. H441 cells were maintained in RPMI 1640 (#11875; Life Technologies) supplemented with 10% FBS, 100 U/ml penicillin G, and 100 ug/ml streptomycin. Cells were grown in a humidified atmosphere with 5% CO2 at 37°C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP were performed as described (Koinuma et al, Mol Cell Biol 29: 172-186, 2009). SMAD3, SMAD4, or TTF-1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
input genome for Smad3 ChIP in A549 cells
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| Data processing |
ChIP-seq reads were aligned to the hg18 genome assembly.
peaks were called using CisGenome version 2 using default parameters.
Genome_build: hg18
Supplementary_files_format_and_content: bed and wig files were generated using CisGenome v2.0.
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| Submission date |
Oct 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Daizo Koinuma |
| E-mail(s) |
[email protected]
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| Organization name |
University of Tokyo
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| Department |
Pathology
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| Street address |
Hongo 7-3-1, Bunkyo-ku
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| City |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
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| Platform ID |
GPL10999 |
| Series (2) |
| GSE51509 |
Smad3, Smad4 and TTF-1/NKX2-1 binding sites in H441/A549 lung cancer cell lines |
| GSE51510 |
Role of TTF-1/NKX2-1, Smad3 and Smad4 on lung cancer cell lines |
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| Relations |
| BioSample |
SAMN02378780 |
| SRA |
SRX366174 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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