|
| Status |
Public on Jul 27, 2014 |
| Title |
Smad4 ChIP-seq, H441/siTTF-1 cells |
| Sample type |
SRA |
| |
|
| Source name |
H441_Smad4_siTTF-1
|
| Organism |
Homo sapiens |
| Characteristics |
ttf-1 expression: depleted by siRNA
cell line: H441
histology: lung adenocarcinoma
chip antibody: SMAD4 [R&D, Catalog#: AF2097]
|
| Treatment protocol |
Cells were treated with 1 ng/ml of TGF-beta3 for 1.5 h.
|
| 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.
|
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
cut-off FDR value for peak calling: 10%
|
| 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.
|
| |
|
| Submission date |
Oct 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Daizo Koinuma |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Tokyo
|
| Department |
Pathology
|
| Street address |
Hongo 7-3-1, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
| |
|
| 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 |
|
| Relations |
| BioSample |
SAMN02378779 |
| SRA |
SRX366173 |
