|
| Status |
Public on Jan 31, 2023 |
| Title |
WBKO_In |
| Sample type |
SRA |
| |
|
| Source name |
islet
|
| Organism |
Mus musculus |
| Characteristics |
tissue: islet
chip antibody: none
genotype: Wtap-betaKO
|
| Growth protocol |
Wtapflox/flox and Wtap-βKO mice were fed with normal chow for 7 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Islets were isolated from pancreatic islets of Wtapflox/flox and Wtap-βKO mice at 7 weeks old. Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany). A total of 2 μg RNAs were pooled from ten Wtapflox/flox mice and nineteen Wtap-βKO 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 |
| |
|
| Data processing |
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(GRCm38/mm10)
Supplementary files format and content: Processed data files; excel; WFF_peaks; WBKO_peaks
|
| |
|
| Submission date |
Oct 12, 2022 |
| Last update date |
Jan 31, 2023 |
| 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) |
| GSE215360 |
The effects of WTAP on m6A mRNA modification pancreatic islets |
|
| Relations |
| BioSample |
SAMN31261094 |
| SRA |
SRX17869360 |
