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Sample GSM3723815 Query DataSets for GSM3723815
Status Public on Apr 17, 2019
Title MDA231: IVCON
Sample type SRA
 
Source name MDA231
Organism Homo sapiens
Characteristics cell line: MDA231 (parental)
cell type: breast cancer cells
rna substrate: None
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 SAMN11433288
SRA SRX5693645

Supplementary file Size Download File type/resource
GSM3723815_IVCON.miR.expre.txt.gz 9.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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