|
| Status |
Public on Apr 17, 2019 |
| Title |
MDA231: IVMS2 |
| Sample type |
SRA |
| |
|
| Source name |
MDA231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA231 (parental)
cell type: breast cancer cells
rna substrate: lncRNA MACC1-AS1-MS2
|
| Treatment protocol |
LncRNA MACC1-AS1-MS2 was in vitro transcribed using T7 RNA polymerase transcription system. RNA was incubated with Amylose resin attached MBP-MCP (MS2 coat protein) at 4°C for 3 h with gentle rotation
|
| Growth protocol |
MDA231 Cells were cultured in cultured DMEM supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 µg/ml streptomycin at 37 °C in a humid environment with 5 % CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MDA231 Cells were lysed in an ice-cold lysis buffer (20 mM Tris•Cl pH7.5, 50 mM NaCl, 5 mM MgCl2, 0.5% NP-40) containing protease inhibitors and RNasin (200 U/mL). Lysates were centrifuged at 12,000 rpm at 4°C for 15 minutes to remove cell debris. Cell lysates were incubated with RNA conjugated Amylose resin at 4°C for 5 h with gentle rotation. After washed with wash buffer, the Amylose resin complexes were eluted with 100 μl lysis buffer containing 10 mmol/L maltose. The eluted samples were further subject to RNA purification for miRNA-seq.
Libaries were prepared for sequencing according to Illumina's protocol. The experiment was performed by the Guangzhou RiboBio co. Ltd in Guangzhou, China.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
miRNA profiling by RNA sequencing
|
| Data processing |
Libraries were sequenced using the Illumina HiSeqTM 2500.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, and mapped to human genome using BWA. Clean reads were compared with a miRBase database (version 21) . The analysis was performed by the Guangzhou RiboBio co. Ltd in Guangzhou, China.
Supplementary_files_format_and_content: Excel files include RPM values for each Sample
|
| |
|
| Submission date |
Apr 16, 2019 |
| Last update date |
Apr 17, 2019 |
| Contact name |
Zhou Yanchun |
| E-mail(s) |
zyc2013st@foxmail.com
|
| Organization name |
Shantou University Medical College
|
| Department |
Pathophysiology
|
| Street address |
Xinling Road
|
| City |
Shantou |
| State/province |
Guangdong |
| ZIP/Postal code |
515041 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE129873 |
Identifcation of lncRNA MACC1-AS1-associated microRNAs in breast cancer cell line MDA231 using MS2-Tagged RNA Affinity Purification and miRNA-Seq |
|
| Relations |
| BioSample |
SAMN11433289 |
| SRA |
SRX5693644 |
