|
| Status |
Public on May 06, 2024 |
| Title |
NingXIANG pig muscle, replicate1, 5-day-old, MeRIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
longissimus dorsi
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: longissimus dorsi
breed: NingXIANG
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific) and the concentration of total RNA were measured by Qubit RNA HS Assay. mRNA was isolated from 75 ug of total RNA using Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific). The purified mRNA was then fragmented in 1X RNA Fragmentation Buffer (Thermo Fisher Scientific) at 70℃ for 5 min. After purification, the fragmented RNA was used for enrichment with 5 ug of m6A antibody (Synaptic Systems) which were previously incubated with 25ul of protein A/G magnetic beads mixture (Thermo Fisher Scientific). The incubation was performed at 4℃ for 4h with rotation. After immunoprecipitation, the magnetic beads were washed 3 times using IP buffer (150 mM NaCl, 10 mM Tris-HCl pH 7.5, 0.1% IGEPAL CA-630 in nuclease-free H2O) for 10 min of each time at 4℃ with rotation. Finally, the m6A modified mRNA fragments were extracted by Trizol reagent and purified with RNA Clean & Concentrator™ Kit (Zymo Research)
After purification, both m6A antibody enriched RNA and partial of unenriched mRNA after fragmentation which was used as input was constructed library using VAHTS® mRNA-seq V3 Library Prep Kit for Illumina(Vazyme) according to the manufacturer’s protocol.
MeRIP-seq
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
NX_1_Peak_Anno_knownGene.txt
|
| Data processing |
Raw sequencing fastq files were assessed for quality, adapter content and duplication rates with FastQC v0.11.9
trimmed using trimmomaticv0.38and aligned with hisat2v2.2.1 to either the piggenome usingsusScr11versions fromdatabasename.
Methylation modification regions were identified by peak calling for each sample separately using exomepeak v2.17.0
the different peak between groups were determined using exomepeak
peaksand different peaks wereannotated to the positionof genesusing ChIPseeker v1.30.2.The motifs were analyzed using homer.
Assembly: susScr11
Supplementary files format and content: tab-delimited txt files include peak counts for each sample.
|
| |
|
| Submission date |
Apr 29, 2024 |
| Last update date |
May 06, 2024 |
| Contact name |
gu hao |
| E-mail(s) |
guhao@hbaas.com
|
| Organization name |
Hubei Academy of Agricultural Sciences
|
| Street address |
29 Nanhu Avenue, Shizishan Street
|
| City |
wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE266121 |
N6-Methyladenosine RNA Modification Regulates the Differential Muscle Development in Large White and Ningxiang Pigs |
|
| Relations |
| BioSample |
SAMN41113931 |
| SRA |
SRX24393639 |
