|
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.
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|
|
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
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|
|
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 |