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Series GSE145390 Query DataSets for GSE145390
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
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.
Overall design 2 replicates, each containing input and IP samples
Contributor(s) Ji S, Niu F, Yang L
Citation(s) 35179492
Submission date Feb 17, 2020
Last update date Mar 15, 2022
Contact name Fugui Niu
Organization name SUSTech
Department Biology
Lab Shengjian Ji
Street address 1088 Xueyuan Avenue
City Shenzhen
State/province Guangdong
ZIP/Postal code 518055
Country China
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (4)
GSM4317639 Retina Input rep1
GSM4317640 Retina input rep2
GSM4317641 Retina Ythdf2 rep1
BioProject PRJNA607064
SRA SRP249709

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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Raw data are available in SRA
Processed data are available on Series record

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