|
| Status |
Public on Jan 22, 2019 |
| Title |
SCNT_FOC+K_1 |
| Sample type |
SRA |
| |
|
| Source name |
SCNT 2-cell embryos injected with Kdm4a mRNA
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6D2F1
tissue: preimplantation embryo
age: 2-cell
genotype: Wild type
|
| Treatment protocol |
Mouse Kdm4a-injected 2-cell and blastocyst SCNT embryos were treated with vehicle or 10μM melatonin.
|
| Growth protocol |
The fresh and vitrified/warmed oocytes were enucleated in M2 medium containing 5μg/ml cytochalasin B. For nuclear transfer, cumulus cells were injected into enucleated oocytes in M2 medium using a piezo-driven micromanipulator (Primetech LTD, Tsuchiura-shi, Japan). After nuclear transfer, the reconstructed embryos were activated for 6 h by 10mM SrCl2, 2 mM EGTA, and 5 μg/ml cytochalasin B in M16 (Millipore) medium and then cultured in KSOM in a humidified atmosphere of 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq experiments with total RNA samples (50~100 embryos) extracted from 2-3 biological replicates were performed. Total RNA was extracted from SCNT_FOC+K, SCNT-CROC+K and SCNT_CROC+K+M embryos using RNeasy Plus Mini Kit (74134, Qiagen) and its amount and quality of the total RNA were evaluated using Bioanalyzer (Agilent). RNA samples with >7.0 RNA Integrity Number (RIN) value were used for RNA-Seq library preparation using combined SMARTer Ultra Low Input RNA cDNA preparation kit (TAKARA) with ScriptSeq v2 kit (Illumina) according to manufacturer’s instruction.
Libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Paired-end sequencing reads were mapped to mm9 mouse genome using STAR tool(v2.5.2b).
After mapping, fragments per kilobase million (FPKM) was calculated by Cufflinks (v2.2.1) tool using the following strand-specific Cuffnorm option: --library-type=fr-second strand.
Functional annotation of differentially expressed genes (DEGs) and enrichment analyses were performed using DAVID (v6.8) and Gene Set Enrichment Analysis (GSEA, v2.2.4), respectively, and genes were considered differentially expressed at the fold change > 3 and FPKM > 5. R (v3.3.2) package was used for statistical analyses and scatter plot generation, and RNA-Seq results were visualized using Integrative Genomics Viewer (IGV).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jan 21, 2019 |
| Last update date |
Jan 23, 2019 |
| Contact name |
Chanhyeok Park |
| E-mail(s) |
chpark0729@gmail.com
|
| Organization name |
Konkuk University
|
| Department |
Stem cell and regeneration biotechnology
|
| Lab |
Hong lab
|
| Street address |
120, Neungdong-ro
|
| City |
Seoul |
| ZIP/Postal code |
05066 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE125389 |
Anti-apoptotic regulation contributes successful nuclear reprogramming using cryopreserved oocytes |
|
| Relations |
| BioSample |
SAMN10784828 |
| SRA |
SRX5273860 |
