|
| Status |
Public on Sep 07, 2020 |
| Title |
S7YICM8_L6 |
| Sample type |
SRA |
| |
|
| Source name |
inner cell mass (ICM)
|
| Organism |
Sus scrofa |
| Characteristics |
replicate: sample S7YICM8 repeat2
tissue: inner cell mass (ICM)
|
| Treatment protocol |
Denuded oocytes were activated using 5 μM ionomycin in TALP-medium (5 minutes) and incubated in 2 mM 6-DMAP for 4 hours in final embryo culture medium supplemented with BSA (for the prevention of the second polar body extrusion). NCSU23 and SOF were used as embryo culture media up to blastocyst stage. At the 5th day of bovine embryo development half of the medium was changed with fresh and equilibrated SOF. The blastocyst rate was calculated in relation to activated oocytes.
|
| Growth protocol |
In vitro maturation of porcine cumulus-oocyte complexes (COCs) was performed in 500 µl of IVM medium (NCSU-23; North Carolina State University Medium-23) in four-well plates (Nunc, NY, USA). Each 500 µl IVM medium consisted of 70 COCs that were matured in HeraCell 150 incubator (Thermo Scientific, MA, USA) under conditions: 5% CO2 in atmosphere, 38.5°C and maximum humidity. The first 24h of porcine IVM included medium supplemented with hormones: 10U PMSG (pregnant mare serum gonadotropin, Chorulon, MSD Animal Health, NL) and 10U hCG (Folligon, MSD Animal Health, NL). The next step included the transfer of COCs to fresh, equilibrated medium without hormones for 20 hours maturation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Takara) was used to generate high-quality cDNA from samples
Nextera XT DNA and Nextera XT Index Kit v2 (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-Seq raw paired-end reads were trimmed with cutadapt
Reads were aligned to Ensembl Sscrofa11.1 procine genome with STAR (v2.7)
BAM files were merged with samtools (v1.10)
Counts were obtained using featureCounts v1.6.3
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Table with gene expression raw reads in csv format.
|
| |
|
| Submission date |
Aug 12, 2020 |
| Last update date |
Sep 07, 2020 |
| Contact name |
Arkadiusz Kajdasz |
| E-mail(s) |
akajdasz@ibch.poznan.pl
|
| Organization name |
Institute of Bioorganic Chemistry PAS
|
| Lab |
Laboratory of Bioinformatics
|
| Street address |
ul. Z. Noskowskiego 12/14
|
| City |
Poznań |
| State/province |
wielkopolskie |
| ZIP/Postal code |
61-704 |
| Country |
Poland |
| |
|
| Platform ID |
GPL26351 |
| Series (2) |
| GSE156148 |
Lipid stores and lipid metabolism associated gene expression in porcine and bovine parthenogenetic embryos revealed by immunostaining and RNA-seq [Ss] |
| GSE156149 |
Lipid stores and lipid metabolism associated gene expression in porcine and bovine parthenogenetic embryos revealed by immunostaining and RNA-seq |
|
| Relations |
| BioSample |
SAMN15804600 |
| SRA |
SRX8935657 |
