|
| Status |
Public on May 06, 2021 |
| Title |
Control_1 |
| Sample type |
SRA |
| |
|
| Source name |
porcine blastocyst_control
|
| Organism |
Sus scrofa |
| Characteristics |
cell type: embryo
cell type: porcine blastocyst
genotype/variation: non-injected control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
non-injected and CARM1-siRNA injected embryos
The libraries were prepared according to the transcriptome differential expression analysis of the control group and the experimrntal group
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Homo sapiens (Version: GRCh38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org). HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: Version GRCh38.p10
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
May 05, 2021 |
| Last update date |
May 07, 2021 |
| Contact name |
Zubing Cao |
| E-mail(s) |
zubingcao@ahau.edu.cn
|
| Organization name |
Anhui Agricultural University
|
| Department |
Animal Science
|
| Street address |
130 changjiang west road
|
| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230036 |
| Country |
China |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE173965 |
Histone arginine methyltransferase CARM1-mediated H3R26me2 is essential for morula-to-blastocyst transition in pigs |
|
| Relations |
| BioSample |
SAMN19028226 |
| SRA |
SRX10798900 |
