|
| Status |
Public on Sep 25, 2016 |
| Title |
Newborn 1 Input |
| Sample type |
SRA |
| |
|
| Source name |
Newborn Input
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Rongchang pig
tissue: liver
age: Postnatal day 0
rip antibody: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was subjected to two rounds of purification using oligo(dT)-coupled magnetic beads according to the manufacturer’s instructions (Ambion), for mRNA isolation. The mRNA was chemically fragmented approximately 150-nucleotide-long using NEBNext® Magnesium RNA Fragmentation Module (NEB #E6150S) according to the manufacturer's protocol. Approximately 5 μg fragmented mRNA was subjected to immunoprecipitation, according to the reported MeRIP protocal.
NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (E7530L, New England Biolabs) was used to construct the library from immunoprecipitated RNA and input RNA according to manufacturer’s published protocol.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
library strategy: MeRIP-Seq
Base-calling with CASAVA.
Adaptor and low quality bases were trimmed with Skewer.
Aligned to pig reference genome Sscrofa10.2.81 downloading from Ensemble (www.ensembl.org) with BWA MEM
Duplicated reads were marked with Samblaster
Only the uniquely mapped (MAPQ>=13) and duplicated alignments were used for peak calling
MACS2 is employed to perform peak calling with a threshold of q 0.05 with insert size of 200 base pair.
Genome_build: Sscrofa10.2.81
Supplementary_files_format_and_content: bw files of paired MeRIP and Input of each replicate.
|
| |
|
| Submission date |
Sep 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shen He |
| E-mail(s) |
heshen7@126.com
|
| Phone |
17628293756
|
| Organization name |
Sichuan Agricultural University
|
| Department |
College of Animal Science and Technology
|
| Lab |
Institute of Animal Genetics and Breeding
|
| Street address |
wenjiang, huimin road 211
|
| City |
Chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE87327 |
Diverse Patterns of N6-methyladenosine mRNA Methylation in Porcine Liver of Postnatal Development Stages |
|
| Relations |
| BioSample |
SAMN05821340 |
| SRA |
SRX2188836 |
