NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4064399 Query DataSets for GSM4064399
Status Public on Dec 31, 2019
Title 252364710488___3
Sample type RNA
 
Source name Omental_Fat___ANGUS___Pasture_Feeding___Replicate_3
Organism Bos taurus
Characteristics fat depot: Omental_Fat
breed: ANGUS
feeding protocol: Pasture_Feeding
replicate number: Replicate_3
age: 259 days
Treatment protocol post-slaughter tissue samples were dissected in an abattoir and snap frozen prior to RNA extraction
Growth protocol 259 d in a feedlot
Extracted molecule total RNA
Extraction protocol RNA was prepared using the phenol chloroform extraction methodology with Trizol reagent
Label Cy3
Label protocol We used the Agilent one colour microarray based gene expression analysis low input Quick Amp labeling. We used an input of 50 ng of total RNA
 
Hybridization protocol 1.65 ug of fragmented, labeled cRNA was prepared for hybridisation. Samples were hybridised to arrays for 17 hours at 45 degree C rotating at 10 rpm in the Agilent hybridisation oven. Arrays were washed using Gene Expression Wash buffer kit in a slide staining dish with slide rack.
Scan protocol Arrays were scanned in the Agilent C scanner using the AgilentHD_GX_1 color protocol
Description OME_ANG_PAST_3
gene expresson after 259 d in a feedlot
Data processing We applied the base-2 log-transformation followed by a normalization using a previously described mixed model approach (Reverter et al. 2004. Bioinformatics 21:1112-1120. https://doi.org/10.1093/bioinformatics/bti124). In brief, the mixed model contained the fixed effect of library sample with 96 levels and the random effects of gene, gene by breed interaction, gene by tissue interaction and residual.
 
Submission date Sep 05, 2019
Last update date Jan 01, 2020
Contact name Sean McWilliam
E-mail(s) [email protected]
Organization name CSIRO
Department Agriculture and Food
Street address 306 Carmody Road
City St Lucia
State/province Queensland
ZIP/Postal code 4067
Country Australia
 
Platform ID GPL11649
Series (1)
GSE136981 Gene expression identifies metabolic and functional differences between intramuscular and subcutaneous adipocytes in cattle

Data table header descriptions
ID_REF
VALUE normalised signal intensity

Data table
ID_REF VALUE
A_73_100002 12.0519
A_73_100009 11.006
A_73_100012 9.25267
A_73_100019 7.45121
A_73_100021 10.5309
A_73_100023 9.23482
A_73_100026 12.0924
A_73_100029 7.3837
A_73_100030 9.03205
A_73_100034 13.1894
A_73_100035 12.1751
A_73_100036 4.61471
A_73_100037 16.8945
A_73_100038 8.67066
A_73_100039 9.96723
A_73_100040 4.32193
A_73_100041 10.4671
A_73_100042 7.03342
A_73_100044 5
A_73_100047 10.3565

Total number of rows: 34227

Table truncated, full table size 683 Kbytes.




Supplementary file Size Download File type/resource
GSM4064399_Ramaciotti_252364710488_S01_GE1_107_Sep09_1_3.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