|
| Status |
Public on Jul 01, 2019 |
| Title |
Ovol2 |
| Sample type |
SRA |
| |
|
| Source name |
MCF10A
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: mammary gland
cell line: MCF10A
lentivirus induction: Ovol2 overexpression
|
| Treatment protocol |
Cells were infected with recombinant lentiviruses expressing Ovol2, Snail and Zeb1 (pHIV-ZsGreen). Six days after transfection, GFP-positive cells were purified by flow cytometry.
|
| Growth protocol |
MCF10A cells were cultured in DMEM/F12(1:1) supplemented with horse serum (5%), epidermal growth factor (10 ng/mL), cholera toxin (100 ng/mL) and insulin (0.023 IU/mL).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using RNAeasy column kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Library construction was performed according to the Illumina TruSeq RNA v2 protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome with Tophat.
Mapped reads are provided as input to Cufflinks, which produces one file of assembled transfrags for each replicate. The assembly files are merged with the reference transcriptome annotation into a unified annotation for further analysis. This merged annotation is quantified in each condition by Cuffdiff, which produces expression data in a set of tabular files.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fragments per kilobase of transcript per million fragments mapped (FPKM) values for each sample .
Supplementary_files_format_and_content: expression abundance EV vs Zeb
Supplementary_files_format_and_content: expression abundance EV vs Snail
Supplementary_files_format_and_content: expression abundance EV vs Ovol2
|
| |
|
| Submission date |
Jul 06, 2015 |
| Last update date |
Jul 01, 2019 |
| Contact name |
Kazuhide Watanabe |
| E-mail(s) |
kazuhide.watanabe@riken.jp
|
| Phone |
+81-045-503-9222
|
| Organization name |
Riken
|
| Department |
Center for Integrative Medical Sciences
|
| Street address |
1-7-22 Suehiro-cho Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE70551 |
Gene expression changes by exogenous expression of epithelial-to-mesenchymal (EMT)-inducing transcription factors (Snail and Zeb1) and mesenchymal-to-epithelial transition (MET)-inducing transcription factor (Ovol2) in MCF10A cells |
|
| Relations |
| BioSample |
SAMN03840671 |
| SRA |
SRX1081835 |
