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Sample GSM1479693 Query DataSets for GSM1479693
Status Public on Nov 22, 2021
Title alpha-amanitin treated 2-cell embryo_8
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 AM8
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 SAMN02990439
SRA SRX681397

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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