|
| Status |
Public on Jan 19, 2023 |
| Title |
Mouse-Hippocampus-WT-RIP-YTHDF2-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Hippocampus
age: post natal day 40
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hippocampus tissus was lysated with lysis buffer in EZ-Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore), then processed following the manuscript. RNA was harvested using Trizol reagent.
The library was constructed by Novogene Corporation (Beijing, China) following their manual.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12)
The MACS2 (version 2.1.0) peak calling software was used to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Homer (Heinz et al., 2010) was used to detect the denovo sequence motif and the matched known motifs.
Peak related genes can be confirmed by PeakAnnotator
Genome_build: GRCm38
|
| |
|
| Submission date |
Apr 09, 2021 |
| Last update date |
Jan 19, 2023 |
| Contact name |
Mengru Zhuang |
| E-mail(s) |
11751018@mail.sustech.edu.cn
|
| Organization name |
Southern University of Science and Technology
|
| Street address |
1088 Xueyuan Avenue, Nanshan District
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE171791 |
Anti-YTHDF2 RIP-Seq to identify YTHDF2 target mRNAs in hippocampus |
|
| Relations |
| BioSample |
SAMN18683583 |
| SRA |
SRX10564407 |
