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Sample GSM5216538 Query DataSets for GSM5216538
Status Public on Mar 27, 2024
Title T24-2-input
Sample type SRA
 
Source name T24
Organism Homo sapiens
Characteristics cell line: T24
genotype: control
rip antibody: none
Extracted molecule total RNA
Extraction protocol RNA fragments were incubated with anti-N6-methyladenosine (m6A) antibodies (Sigma-Aldrich, Burlington, USA) inimmunoprecipitation (IP) buffer for 2 h at 4℃. The samples were then washed with low-salt precipitation buffer and high-salt buffer thrice continuously. RNA was extracted using a phenol-chloroform lysate to obtain a purified product.
The purified RNA was collected for the generation of an RNA-seq library with NEBNext R Ultra™ RNA Library Prep Kit (New England Biolabs, MA, USA). The quality of the library was done using Bioptic Qsep100 analyzer and sequencing was done using NovaSeq's high-throughput sequencing platform
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing 150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38 by using Bowtie2.
Only unique mapping paired reads were sorted using SAMtools and kept for subsequent analysis.
Peaks of each samples and differential methylation peak were called using the exomePeak R-package.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: peak files
 
Submission date Mar 29, 2021
Last update date Mar 27, 2024
Contact name Zengnan Mo
E-mail(s) mozengnan@gxmu.edu.cn
Phone 15188577508
Organization name Guangxi Medical University
Department Center for Genomics and Personalized Medicine
Street address Zhongshan Street
City Nanning
State/province Guangxi
ZIP/Postal code 530021
Country China
 
Platform ID GPL24676
Series (2)
GSE171023 Potential Roles of IGF2BP3 in Bladder Cancer [m6A-seq]
GSE171024 Potential Roles of IGF2BP3 in Bladder Cancer
Relations
BioSample SAMN18524352
SRA SRX10465416

Supplementary file Size Download File type/resource
GSM5216538_T24-2-input.sorted.bam.forward.bw 2.1 Mb (ftp)(http) BW
GSM5216538_T24-2-input.sorted.bam.reverse.bw 1.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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