|
| Status |
Public on Apr 29, 2019 |
| Title |
IV-D-OC1 |
| Sample type |
SRA |
| |
|
| Source name |
oocytes
|
| Organism |
Sus scrofa |
| Characteristics |
strain: Duroc
developmental stage: pre-implantation
method: in vivo
|
| Growth protocol |
Cloned embryos were cultured in the PZM3 medium in a low-oxygen humidified atmosphere containing 5% CO2, 5% O2, and 90% N2 at 38.5°C. In vivo matured oocytes and embryos were collected immediately after rushing out of the sows with DPBS. Morphologically normal embryos with few fragments were selected for RNA-seq.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
cDNA was generated and amplified with the SMART-Seq® v4 Ultra Low Input RNA Kit for Sequencing.
RNA libraries were generated using NEBNext Ultra RNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
DEG_Genes_ExpMat_FPKM.txt
|
| Data processing |
Paired-end clean reads were aligned to the porcine reference genome using Hisat2 v2.0.4.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using DESeq or DEGSeq.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for differentially expressed genes of all samples
|
| |
|
| Submission date |
Jan 27, 2019 |
| Last update date |
Apr 29, 2019 |
| Contact name |
Xiaoyan He |
| Organization name |
South China Agricultural University
|
| Street address |
No.483 Wushan Road, Tianhe District
|
| City |
Guangzhou |
| ZIP/Postal code |
510642 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE125706 |
Characterization and comparative analyses of transcriptomes of cloned and in vivo fertilized porcine pre-implantation embryos |
|
| Relations |
| BioSample |
SAMN10826841 |
| SRA |
SRX5296591 |
