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Sample GSM7092740 Query DataSets for GSM7092740
Status Public on Jan 14, 2024
Title WFF_heart_In
Sample type SRA
 
Source name heart
Organism Mus musculus
Characteristics tissue: heart
chip antibody: none
genotype: Wtapflox/flox
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from the hearts of Wtapflox/flox and Wtap-CKO mice at 4 days old. A total of 300 μg RNAs were pooled from seven Wtapflox/flox mice and eight Wtap-CKO mice, respectively.
Fragmented RNA (~100 nt) was incubated for 2 hr at 4oC with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols.
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description WFF_peak.txt
Data processing library strategy: meRIP-seq
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11).
Index of the reference genome was built using BWA v0.7.12 and clean reads were aligned to the reference genome using BWA mem v 0.7.12.
exomePeak R package (version 2.16.0) was used for the m6A peak identification
The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1).
GO enrichment analysis was implemented by the GOseq R package.
Assembly: mouse reference genome(GRCm39)
Supplementary files format and content: Processed data files; excel; WFF_peak; WCKO_peak
 
Submission date Mar 12, 2023
Last update date Jan 14, 2024
Contact name Zheng Chen
E-mail(s) chenzheng@hit.edu.cn
Phone +8645186402029
Organization name Harbin Institute of Technology
Street address 92 Xidazhijie Harbin Institute of Technology
City Harbin
State/province Heilongjiang
ZIP/Postal code 150001
Country China
 
Platform ID GPL24247
Series (1)
GSE227174 The effects of WTAP on m6A mRNA modification in the heart [meRIP-seq]
Relations
BioSample SAMN33730476
SRA SRX19644340

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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