|
| Status |
Public on Nov 22, 2021 |
| Title |
alpha-amanitin treated 2-cell embryo_2 |
| Sample type |
SRA |
| |
|
| Source name |
alpha-amanitin treated 2-cell embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6xDBA
developmental stage: 2-cell embryo
|
| Treatment protocol |
control MO injected, in vitro matured- and fertilized- zygotes at 4hpf were cultured with 0.1mg/ml α-amantin (Sigma) and derived 2-cell embryos were collected 29hpf
|
| Growth protocol |
48h post injection of 5 IU pregnant mare serum fully grown oocytes at the germinal vesicle stage were obtained from ovaries of 6-8 weeks old F1(C57BL/6×DBA) female mice and transferred to M2 medium without BSA, supplemented with 0.2 mM 3-isobutyl-1-methylxanthine (IBMX; Sigma-Aldrich). After 10 min of Hoechst 33342 (0.05 μg/ml) incubation SN type GVOs were injected with morpholinos designed against Tet1-3 enzymes (Gene Tools, 100 μM, see table S1) co-injected with Dextran-tetramethyl-rhodamine (Invitrogen, 3000 MW, 100 μg/ml). Morpholino injected SN GVOs were washed in IMBX free α-MEM medium supplemented with 5% FBS and 10 ng/ml EGF and incubated in a humidified atmosphere with 6% CO2, 5% O2 and 89% N2 at 37 °C for 16-18 h to complete meiotic maturation. Sperm was isolated from the cauda epididymis of adult F1(C57BL/6×DBA) male mice and capacitated by pre-incubation for 1.5 h in pre-gassed HTF medium. In vitro matured oocytes were collected 16-18 h post injection of morpholinos. Mature MII oocytes were placed into a 100 μl drop of KSOM medium with capacitated sperm and incubated at 37 °C in a humidified atmosphere of 6% CO2, 5% O2 and 89% N2. 2-cell embryos were collected 29 hours following in vitro fertilization.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
2-cell embryos were collected 29 hours following in vitro fertilization and zona pellucida was removed from 2-cell embryos. Libraries were constructed using Clontech SMARTer Ultra Low Input RNA Kit, followed by NEBNext DNA Library Prep Master Mix Set
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
AM2
|
| Data processing |
Reads were mapped to mouse reference genome mm10, depleted for sex chromosomes with STAR2.5.1b using default settings. Genes from RefSeq database that have at least ten reads in 50% of the embryos of one condition were used for further analysis. Differentially expressed genes were obtained using DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: FPM.txt: Tab-delimited text file includes FPM values.
|
| |
|
| Submission date |
Aug 14, 2014 |
| Last update date |
Nov 22, 2021 |
| Contact name |
Julia Arand |
| E-mail(s) |
[email protected]
|
| Organization name |
Medical University of Vienna
|
| Street address |
Schwarzspanierstr. 16
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE57063 |
Tet enzymes are essential for embryogenesis and completion of embryonic genome activation |
|
| Relations |
| BioSample |
SAMN02990433 |
| SRA |
SRX681391 |
