NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1194936 Query DataSets for GSM1194936
Status Public on Sep 01, 2013
Title Cumulus_clone_extraembryonic_E6.5_rep2
Sample type RNA
 
Source name E6.5 cumulus clone, extraembryonic
Organism Mus musculus
Characteristics gender: female
donor cell: cumulus cell
tissue: extraembryonic
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 cumulus clone, extraembryonic, replicate2
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 -0.99981785
A_52_P580582 -0.117768764
A_52_P403405 -1.2505283
A_52_P819156 -0.4842615
A_51_P331831 0.40711308
A_51_P430630 0.24239779
A_52_P502357 -1.0123911
A_52_P299964 -0.93486357
A_51_P356389 0.53303003
A_52_P684402 -0.6585629
A_51_P414208 -1.2584009
A_51_P280918 -0.004981756
A_52_P613688 0.43363452
A_52_P258194 -0.65349245
A_52_P229271 0.032057524
A_52_P214630 0.14535189
A_52_P579519 -0.002334356
A_52_P979997 -0.9992342
A_52_P453864 -0.7027426
A_52_P655842 -1.2948446

Total number of rows: 41265

Table truncated, full table size 971 Kbytes.




Supplementary file Size Download File type/resource
GSM1194936_CC2X_E6.5.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap