|
| Status |
Public on Jul 27, 2014 |
| Title |
A549 cells infected with Ad-TTF-1, TGF-beta treated |
| Sample type |
SRA |
| |
|
| Source name |
A549 cells infected with Ad-TTF-1, TGF-beta treated
|
| Organism |
Homo sapiens |
| Characteristics |
ttf-1 expression: exogenous expression
treatment: TGF-beta
histology: lung adenocarcinoma
|
| Treatment protocol |
Cells were treated with 1 ng/ml of TGF-beta3 for 24 h without starvation.
|
| 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. Cells were grown in a humidified atmosphere with 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using RNeasy mini column (QIAGEN) with DNaseI treatment. PolyA(+) RNA was selected by Dynabeads mRNA DIRECT Micro Kit (Thermo Scientific).
Libraries were prepared using Ion Total RNA-seq kit v2 (Thermo Scientific). Sequencing was performed using Ion PI Chip Kit v2, PI Template OT2 200 Kit v3 and Ion PI Sequencing 200 Kit v3 (Thermo Scientific).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
TTF-1 expressed, stimulated with TGF-beta
|
| Data processing |
RNA-seq reads were processed by Tophat2 (version 2.0.10) and Bowtie2 (version 2.1.0) using hg19 version of index files.
parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G
Genome_build: hg19
Supplementary_files_format_and_content: FPKM calculation was performed by using Cuffdiff (cufflinks version 2.1.1, with options -m 200 -u). Expression data of the four samples were summarized into single processed file by Cuffdiff.
|
| |
|
| Submission date |
Mar 31, 2014 |
| Last update date |
May 15, 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 |
| |
|
| Platform ID |
GPL17303 |
| Series (2) |
| GSE51510 |
Role of TTF-1/NKX2-1, Smad3 and Smad4 on lung cancer cell lines |
| GSE56356 |
Effect of TTF-1/NKX2-1 expression on TGF-beta induced gene expression in A549 lung cancer cell line. |
|
| Relations |
| BioSample |
SAMN02712132 |
| SRA |
SRX504180 |
