|
| Status |
Public on Jun 01, 2017 |
| Title |
FOXN3_iRIP-Seq_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 Cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF-7
|
| Treatment protocol |
Treated with antibodies against FOXN3.
|
| Growth protocol |
Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a humidified incubator equilibrated with 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
chloroform extraction
One microliter of glycogen (10 mg/ml stock) was added and RNAs were precipitated by adding 3 volumes of ethanol and dissolved in 10.5 μl water. The recovered RNAs were used to generate paired-end sequencing library with Truseq small RNA library preparation kit (Illumina) following the manufacturer’s instruction.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
iRIP-Seq data for FOXN3 replicate2.
|
| Data processing |
base-calling: Phred.
alignment: bowtie2 for ChIP-Seq; TopHat2 for RIP-Seq.
peak-calling: MACS2 for ChIP-Seq; CIMS and Piranha for RIP-Seq.
ChIPseeker for the annotation of peaks.
Genome_build: ChIP-Seq: hg19; RIP-Seq: hg38.
Supplementary_files_format_and_content: bigwig (bw): The signal intensity of binding. Bed files for RIP-Seq.
|
| |
|
| Submission date |
Jan 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Wanjin Li |
| E-mail(s) |
wanjin_li@yeah.net
|
| Phone |
13622157177
|
| Organization name |
Peking University Health Science Center
|
| Street address |
No. 38, Xueyuan road.
|
| City |
Beijing |
| ZIP/Postal code |
100191 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE93780 |
FOXN3 and SIN3A ChIP-Seq; FOXN3 and IgG iRIP-Seq |
| GSE93781 |
FOXN3 Enlists NEAT1-containing SIN3A Complex to Regulate Mammary Epithelium Differentiation and Promote Breast Cancer Metastasis |
|
| Relations |
| BioSample |
SAMN06238146 |
| SRA |
SRX2582731 |
