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| Status |
Public on Jan 19, 2023 |
| Title |
Anti-YTHDF2 RIP-Seq to identify YTHDF2 target mRNAs in hippocampus |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
To identify the target mRNAs of the m6A reader protein YTHDF2 in mouse hippocampus, we carired out anti YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from P40 wild type mouse hippocampus was pulled down by rabbit polyclonal anti-YTHDF2 (proteintech) and then sequenced on Illumina Novaseq 6000. The filtered reads were aligned to the mouse reference genome (GRCm38) using BWA mem (v 0.7.12).Then the MACS2 (version 2.1.0) peak calling software was used to identify regions of IP enrichment over background, followed by the motif detected by Homer (Heinz et al., 2010). Peak related genes are then confirmed by PeakAnnotator. Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified. Finally, Biological replicates of anti-YTHDF2 RIP-Seq identified 408 mRNAs transcripts. This study provides gene lists which shows mRNA binding with YTHDF2 in mouse hippocampus.
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| Overall design |
2 replicates, each containing input and IP samples
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| |
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| Contributor(s) |
Zhuang M, Liang F, Ji S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Apr 09, 2021 |
| Last update date |
Jan 19, 2023 |
| Contact name |
Mengru Zhuang |
| E-mail(s) |
11751018@mail.sustech.edu.cn
|
| Organization name |
Southern University of Science and Technology
|
| Street address |
1088 Xueyuan Avenue, Nanshan District
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA720917 |
| SRA |
SRP314229 |
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