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Sample GSM6805778 Query DataSets for GSM6805778
Status Public on Dec 01, 2023
Title Control (Pull down)
Sample type SRA
 
Source name BT549
Organism Homo sapiens
Characteristics cell line: BT549
cell type: breast cancer cells
genotype: SNHG15-MS2 overexpression
treatment: Amylose resin
Treatment protocol Cell lysates were prepared and then incubated with Amylose resin coated with MBP-MCP (MS2 coat protein) or Amylose resin at 4°C for 5 h in the presence of RNasin (200 U/mL) and protease inhibitors. After incubation, the supernatant was removed by a short centrifugation and the beads were washed three times in ice-cold lysis buffer.
Growth protocol BT549-SNHG15-MS2 Cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100U/ml penicillin, and 100 µg/ml streptomycin at 37 °C in a humid environment with 5 % CO2
Extracted molecule total RNA
Extraction protocol the co-precipitated RNAs were extracted using mirVana™ miRNA Isolation Kit following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using QIAseq miRNA Library Kit.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NovaSeq 6000
 
Description miRNA profiling by RNA sequencing
Data processing Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Fastx.
Clean reads were compared with GRCh38.The analysis was performed by the Shanghai Biotechnology Corporation.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited files include TPM values for each Sample
 
Submission date Dec 08, 2022
Last update date Dec 01, 2023
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 GPL24676
Series (1)
GSE220496 Identification of SNHG15-associated microRNAs in SNHG15 overexpression BT549 cells using miRNA-Seq
Relations
BioSample SAMN32109497
SRA SRX18537404

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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