|
| Status |
Public on Mar 27, 2024 |
| Title |
T24-ko1-IP |
| Sample type |
SRA |
| |
|
| Source name |
T24
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T24
genotype: IGF2BP3 knockout
rip antibody: anti-N6-methyladenosine (m6A) antibodies (Sigma-Aldrich, Burlington, USA)
|
| 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 |
SAMN18524347 |
| SRA |
SRX10465421 |
