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Sample GSM1162495 Query DataSets for GSM1162495
Status Public on Jan 08, 2014
Title 0548_1XUF
Sample type RNA
 
Channel 1
Source name Liver, 1XUF 3 weeks
Organism Bos taurus
Characteristics milking frequency: 1X (once-daily)
feeding level: UF (under-fed)
Treatment protocol Cows were allocated to one of four treatments; twice-daily milking and adequately-fed (2XAF), 2X and under-fed (fed 60% of requirements; 2XUF), once-daily milking AF (1XAF) or 1XUF at approx wk 5 postpartum. Treatments lastest for 3 weeks and liver tissue was then biopsied.
Extracted molecule total RNA
Extraction protocol Liver tissue was homogenised in Qiagen buffer RLT (QIAGEN GmbH, QIAGEN, Hilden, Germany) using a TissueLyser instrument (QIAGEN).
Label Cy5
Label protocol 150ng of total RNA was labelled with Cy5 using an Agilent Low Input Quick Amp (LIQA) kit for each experimental sample, and labelled cRNA was then purified on column, quantified and dye coupling efficiency measured using the Nanodrop (Nanodrop Technologies, Wilmington, DE) instrument. Equimolar amounts of each sample were pooled to generate a reference which was labelled with Cy3 as above.
 
Channel 2
Source name pooled liver
Organism Bos taurus
Characteristics treatment: pooled 2X, 1X, AF, UF
Treatment protocol Cows were allocated to one of four treatments; twice-daily milking and adequately-fed (2XAF), 2X and under-fed (fed 60% of requirements; 2XUF), once-daily milking AF (1XAF) or 1XUF at approx wk 5 postpartum. Treatments lastest for 3 weeks and liver tissue was then biopsied.
Extracted molecule total RNA
Extraction protocol Liver tissue was homogenised in Qiagen buffer RLT (QIAGEN GmbH, QIAGEN, Hilden, Germany) using a TissueLyser instrument (QIAGEN).
Label Cy3
Label protocol 150ng of total RNA was labelled with Cy5 using an Agilent Low Input Quick Amp (LIQA) kit for each experimental sample, and labelled cRNA was then purified on column, quantified and dye coupling efficiency measured using the Nanodrop (Nanodrop Technologies, Wilmington, DE) instrument. Equimolar amounts of each sample were pooled to generate a reference which was labelled with Cy3 as above.
 
 
Hybridization protocol 825ng of both Cy3 and Cy5 labelled cRNA was used for microarray hybridisation using the Agilent Gene Expression Hybridisation Kit (60-mer oligo microarray protocol version 4.0) (Agilent Technologies, Bioresearch Solutions Unit, 3500 Deer Creek Road, Palo Alto, CA 94034, USA). Dye-labelled, fragmented cRNA was then added to each Agilent 44k 60-mer oligonucleotide microarray, hybridised over night (17 hours), washed and allowed to air dry.
Scan protocol Arrays were scanned using the Agilent SureScan microarray scanner at 5uM resolution.
Description Biological Replicate 10 of 11; 1XUF
Data processing Agilent feature extraction software version 10.1 was used to analyse the scanned Agilent microarray. The 45 scanned microarray image files were uploaded to the feature extraction software. Using the design file (015354) the feature extraction software locates features and converts the extracted data from each feature into a quantitative log ratio. The software removes pixel outliers, does statistics on the non outlier pixels, subtracts background from features and flags any outlier features. The software was then used to perform a LOWESS (locally weighted linear regression analysis) dye normalisation and to calculate a p-value for each feature. Microarray data were imported into Genespring GX 12.5 (Agilent, Palo Alto, CA, USA) and filtered by presence and raw intensity (20th - 100th percentile) before generating a gene level experiment that averaged the expression of probes annotated to the same gene which was then exported for analysis.
 
Submission date Jun 13, 2013
Last update date Jan 08, 2014
Contact name Talia Grala
E-mail(s) [email protected]
Organization name DairyNZ
Street address 3 Symonds St
City Auckland
ZIP/Postal code 1010
Country New Zealand
 
Platform ID GPL9712
Series (1)
GSE47925 Effects on the hepatic transcriptome due to caloric restriction are not altered by milking frequency

Data table header descriptions
ID_REF
VALUE lowess normalised log2 ratio (test/ref)

Data table
ID_REF VALUE
A_73_100002 -1.19125
A_73_100004 0.366232
A_73_100005 -0.06224
A_73_100006 0.352781
A_73_100009 -0.90254
A_73_100011 -0.47121
A_73_100012 -0.2236
A_73_100016 0.222892
A_73_100019 0.439588
A_73_100021 -0.05408
A_73_100023 0.477192
A_73_100024 0.07305
A_73_100025 -0.51734
A_73_100026 0.119794
A_73_100028 -0.65117
A_73_100034 0.013923
A_73_100035 -0.21078
A_73_100037 0.743635
A_73_100039 0.130486
A_73_100041 -0.10694

Total number of rows: 10301

Table truncated, full table size 210 Kbytes.




Supplementary file Size Download File type/resource
GSM1162495_R_251535410202_Sep09_1_2_0548_1XUF.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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