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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 15, 2022 |
| Title |
Anti YTHDF2 RIP-seq to identify YTHDF2 target mRNAs in P0 mouse retinas |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To identify the target mRNAs of the m6A reader protein YTHDF2, we carired out anti YTHDF2 RNA Immunoprecipitation (RIP) followed by RNA-sequencencing. Using EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), RNA from P0 wild type mouse retinas was pulled down by rabbit polyclonal anti-YTHDF2 (proteintech) and then sequenced on Illumina HiSeq3000 platform. The filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5 with default parameters. The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads, which was further normalized to calculate FPKM. To determine which gene is enriched, we computed the FPKM from RIP elute to input and any fold change greater than 2 was considered enriched. Finally, Biological replicates of anti-YTHDF2 RIP-Seq identified 1639 transcripts. This study provides a gene list which shows mRNA binding with YTHDF2 in mouse retina.
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| Overall design |
2 replicates, each containing input and IP samples
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| Contributor(s) |
Ji S, Niu F, Yang L |
| Citation(s) |
35179492 |
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| Submission date |
Feb 17, 2020 |
| Last update date |
Mar 15, 2022 |
| Contact name |
Fugui Niu |
| E-mail(s) |
nfg19951025@gmail.com
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| Organization name |
SUSTech
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| Department |
Biology
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| Lab |
Shengjian Ji
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| Street address |
1088 Xueyuan Avenue
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platforms (1) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA607064 |
| SRA |
SRP249709 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE145390_gene_FPKM.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE145390_gene_count.txt.gz |
945.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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