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Sample GSM1194974 Query DataSets for GSM1194974
Status Public on Sep 01, 2013
Title IVF_control_female_blastocyst_rep2
Sample type RNA
Source name IVF control female, blastocyst
Organism Mus musculus
Characteristics gender: female
donor cell: IVF
tissue: blastocyst
embryonic day: E4.0
Treatment protocol Embryos that reached the blastocyst (E4.0) stage were used to extract total RNA.
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 IVF control female, blastocyst, 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
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)
GSE49172 Comparative gene expression analyses using E4.0 cloned blastocysts
GSE49173 Donor cell type-specific gene expression in embryonic but not extraembryonic tissues of postimplantation embryos cloned from somatic cells

Data table header descriptions
VALUE Normalized data expressed in log2 scale.

Data table
A_52_P616356 -2.1748552
A_52_P580582 0.42161894
A_52_P403405 -3.4313269
A_52_P819156 2.743857
A_51_P331831 0.21756363
A_51_P430630 0.5758767
A_52_P502357 -0.15162754
A_52_P299964 0.14677191
A_51_P356389 -0.7181511
A_52_P684402 -0.70351124
A_51_P414208 0.11143398
A_51_P280918 0.29933357
A_52_P613688 0.41640806
A_52_P258194 0.25209618
A_52_P229271 -0.2700491
A_52_P214630 -2.1424417
A_52_P579519 -0.83413696
A_52_P979997 -2.200739
A_52_P453864 -2.1987524
A_52_P655842 -0.019683361

Total number of rows: 41265

Table truncated, full table size 948 Kbytes.

Supplementary file Size Download File type/resource
GSM1194974_IVF2_f_blastocyst.txt.gz 7.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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