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Sample GSM823843 Query DataSets for GSM823843
Status Public on Feb 29, 2012
Title Array 30_vivo_16-cell rep3
Sample type RNA
 
Channel 1
Source name Blastocyst cultured in vivo until 16-cell stage
Organism Bos taurus
Characteristics sample type: in_vivo
breed (cattle): Simmental
reproductive status (cattle): Heifer
Extracted molecule total RNA
Extraction protocol Total RNA extraction was performed using the PicoPure RNA Isolation Kit (ARCTURS, Munich, Germany) according to the manufacturer's instruction.
Label Cy5
Label protocol Amplification of RNA has been done using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
Labelling aRNA was performed using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.
 
Channel 2
Source name in vivo control blastocyst
Organism Bos taurus
Characteristics sample type: in_vivo
breed (cattle): Simmental
reproductive status (cattle): Heifer
Extracted molecule total RNA
Extraction protocol Total RNA extraction was performed using the PicoPure RNA Isolation Kit (ARCTURS, Munich, Germany) according to the manufacturer's instruction.
Label Cy3
Label protocol Amplification of RNA has been done using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
Labelling aRNA was performed using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.
 
 
Hybridization protocol A total of 825 ng of each labeled sample were incubated in a solution containing 2X blocking agent and 1X fragmentation buffer in a volume of 55 μl at 65 °C for 15 min, and were then put on ice. Fifty-five microliters of 2X GEx Hybridization Buffer HI-RPM was added for a final volume of 110 μl. The hybridization mix was added onto the array and hybridization was performed at 65 °C for 17 hr using an Agilent Hybridization chamber in a rotating oven
Scan protocol Slides were scanned using Agilent’s High-Resolution C Scanner (Agilent Technologies, CA, USA) and features were extracted with the Agilent's Feature Extraction software (Agilent Technologies, CA, USA).
Description Array 30
Data processing Data were submitted to a simple background correction, a Loess within array normalization and a Quantile between array normalization.
 
Submission date Oct 28, 2011
Last update date Feb 29, 2012
Contact name Ahmed Gad
E-mail(s) [email protected]
Organization name Colorado State University
Department Biomedical Sciences
Lab ARBL
Street address 3107 Rampart Rd
City Fort Collins
State/province Colorado
ZIP/Postal code 80521
Country USA
 
Platform ID GPL13226
Series (1)
GSE33314 Gene expression analysis of bovine blastocyst produced under alternative in vivo and in vitro culture conditions during EGA time

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
EMBV3_00001 0.043331749
EMBV3_00002 0.002376535
EMBV3_00003 -0.151953892
EMBV3_00004 -0.721329966
EMBV3_00005 -0.557018959
EMBV3_00006 -0.168124733
EMBV3_00007 0.589471189
EMBV3_00008 -1.089257965
EMBV3_00009 0.507774131
EMBV3_00010 0.182630257
EMBV3_00011 -0.118729267
EMBV3_00012 0.210968797
EMBV3_00013 -0.190601614
EMBV3_00014 -0.631416833
EMBV3_00015 -0.458055285
EMBV3_00016 0.155404528
EMBV3_00017 0.354391083
EMBV3_00018 -0.484236135
EMBV3_00019 0.089305182
EMBV3_00020 -0.862262883

Total number of rows: 43794

Table truncated, full table size 1043 Kbytes.




Supplementary file Size Download File type/resource
GSM823843_Q3_5.txt.gz 11.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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