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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
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
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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