|
| Status |
Public on Jan 17, 2020 |
| Title |
RNA-Seq_MCF7_siCARM1-1_CTL_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
treatment: ethanol+siRNA
|
| Treatment protocol |
MCF7 cells were maintained in stripping medium (phenol red free) for three days before treating with or without estrogen (E2, 10-7 M) for 6h.
|
| Growth protocol |
MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality. RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: hg19
|
| |
|
| Submission date |
Dec 27, 2018 |
| Last update date |
Jan 17, 2020 |
| Contact name |
Jiancheng Ding |
| E-mail(s) |
[email protected]
|
| Organization name |
Xiamen University
|
| Street address |
School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road
|
| City |
Xiamen |
| State/province |
Fujian |
| ZIP/Postal code |
361102 |
| Country |
China |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE124447 |
A hypermethylation strategy utilized by enhancer-bound CARM1 to promote estrogen receptor a-dependent transcriptional activation and breast carcinogenesis (RNA-seq) |
| GSE124449 |
A hypermethylation strategy utilized by enhancer-bound CARM1 to promote estrogen receptor a-dependent transcriptional activation and breast carcinogenesis |
|
| Relations |
| BioSample |
SAMN10658645 |
| SRA |
SRX5185588 |
