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Sample GSM1194955 Query DataSets for GSM1194955
Status Public on Sep 01, 2013
Title IVF_control_male_embryonic_E6.5_rep3
Sample type RNA
 
Source name E6.5 IVF control, male, embryonic
Organism Mus musculus
Characteristics gender: male
donor cell: IVF
tissue: embryonic
embryonic day: E6.5
Treatment protocol Embryos that reached the 2-cell stage were transferred into the oviducts of ICR recipient mice at day 1 of pseudopregnancy (the day a copulatory plug was observed after mating with a vasectomized male mouse). On day 7 of pregnancy, corresponding to E6.5, the implanted embryos were recovered carefully from the uteri and isolated from decidua using fine forceps and a needle under a dissecting microscope. After incubation in PBS with 0.25% pancreatin and 0.05% trypsin for 10 minutes at 4 °C, embryos were transferred to DMEM containing 10% FBS and then the visceral endoderm layer was detached from epiblast or extraembryonic ectoderm by being gently aspirated through a mouth pipette several times. Thereafter, the epiblast was separated from the extraembryonic ectoderm using a fine tungsten needle. Isolated epiblasts or extraembryonic regions (extraembryonic ectoderm and ectoplacental cone) were subjected to microarray gene analyses.
Growth protocol In vitro fertilized (IVF) or cloned embryos were cultured in potassium modified simplex optimization medium (KSOM) at 37.5 ºC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with TRIzol (Life Technologies) from epiblasts or extraembryonic regions derived from single embryos and subjected to linear amplification using TargetAmp Two-Round Aminoallyl-aRNA Amplification Kits (Epicentre Biotechnologies).
Label Cy3
Label protocol 5.0 ug of amplified RNA was labelled with Cianine-3 (Cy3) dye (GE Healthcare) for 90 minutes at RT. Labelled RNAs were purified with RNeasy MinElute kit (Qiagen) and checked with the NanoDrop ND-1000 Spectrophotometer
 
Hybridization protocol 1.65ug Cy3-labelled RNAs were fragmented at 60°C for 30 minutes and hybridized at 65°C for 17 hours according to manufacture's instructions.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).
Description E6.5 IVF control, male, embryonic, replicate3
Data processing The scanned images of microarray slides were processed using Feature Extraction software 10.5.1 (Agilent Technologies). All raw data were loaded into Gene Spring GX 12.5 (Agilent Technologies) and transformed by default setting.
 
Submission date Jul 24, 2013
Last update date Sep 01, 2013
Contact name Kimiko Inoue
E-mail(s) kimiko.inoue@riken.jp
Organization name BRC, RIKEN
Department Bioresource Engineering Division
Street address 3-1-1 Koyadai
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-0074
Country Japan
 
Platform ID GPL7202
Series (2)
GSE49171 Comparative gene expression analyses using post-implanted E6.5 cloned embryos
GSE49173 Donor cell type-specific gene expression in embryonic but not extraembryonic tissues of postimplantation embryos cloned from somatic cells

Data table header descriptions
ID_REF
VALUE Normalized data expressed in log2 scale for mean values of IVF controls.

Data table
ID_REF VALUE
A_52_P616356 0.18090153
A_52_P580582 1.0105782
A_52_P403405 1.0041809
A_52_P819156 0.18111467
A_51_P331831 -0.0345484
A_51_P430630 0.18125391
A_52_P502357 0.18165922
A_52_P299964 0.18161774
A_51_P356389 -0.770988
A_52_P684402 0.07260704
A_51_P414208 0.18216944
A_51_P280918 -0.04652822
A_52_P613688 0.28899038
A_52_P258194 0.97976303
A_52_P229271 -0.098258734
A_52_P214630 0.80817825
A_52_P579519 -0.21059513
A_52_P979997 0.18375635
A_52_P453864 0.18399239
A_52_P655842 0.18454742

Total number of rows: 41265

Table truncated, full table size 969 Kbytes.




Supplementary file Size Download File type/resource
GSM1194955_IVF_m_3E_E6.5.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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