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Sample GSM688565 Query DataSets for GSM688565
Status Public on May 10, 2011
Title BA02_liver_hibernating_N03-056
Sample type RNA
 
Source name liver, hibernating
Organism Ursus americanus
Characteristics tissue type: liver
gender: male
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen tissues stored at -80 C by grinding in liquid nitrogen with mortar and pestle and using RNeasy Kit (Qiagen). Skeletal muscle tissue was treated by proteinase K and RNA was extracted by using RNeasy Fibrous Tissue Kit (Qiagen). All RNA samples were processed by DNase I (Qiagen) treatment. For cDNA library construction, mRNA was selected from total RNA with the oligo(dT) cellulose by the use of Poly(A) Purist Kit (Ambion).
Label 33P
Label protocol Samples of total RNA were linearly amplified with Illumina TotalPrep RNA Amplification Kit (Ambion), and 1.6 μg of the amplified RNA was labeled with 65 μCi of [33P]dCTP. All RNA samples were amplified, labeled and hybridized in the same batch.
 
Hybridization protocol The hybridization was carried out for 18 hours at 42°C in 4 ml of MicroHyb buffer (Invitrogen). Filters were rinsed at room temperature with 2× SSC/1% SDS to remove residual probe and MicroHyb solution and then transferred to preheated wash solutions in a temperature-controlled shaking water bath. Filters were washed twice for 30 min in 1.5 l of 2× SSC/1% SDS at 50°C and then once for 30 min in 1.5 l of 0.5× SSC/1% SDS at 55°C.
Scan protocol Filters were then exposed to phosphorimager screens for four days and scanned at 50-µm resolution in a Storm Phosphorimager.
Description liver tissue from hibernating black bear
Data processing Image analysis was performed with the ImaGene program (Biodiscovery). Only nonempty spots with signal median density exceeding double background median in all individuals were included in the analysis. Background corrected signal was obtained by subtracting local background median density from signal median density. Background corrected signals were divided by their median on the array to obtain the normalized median densities representing the normalized expression values.
 
Submission date Mar 10, 2011
Last update date May 10, 2011
Contact name Haifang Wang
Organization name Shanghai institute for biology science
Department CAS-MPG Partner institute for Computational Biology
Street address 320 yueyang road
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL13263
Series (1)
GSE27875 Modulation of gene expression in heart and liver of hibernating black bears (Ursus americanus)

Data table header descriptions
ID_REF
VALUE normalized expression value

Data table
ID_REF VALUE
1 0.358
2 1.257
3 0.926
4 0.490
5 1.365
6 0.723
7 0.395
8 1.076
9 1.962
10 0.528
11 0.629
12 2.143
13 5.154
14 1.914
15 2.406
16 3.772
17 1063.746
18 0.002
19 0.828
20 0.569

Total number of rows: 9600

Table truncated, full table size 103 Kbytes.




Supplementary file Size Download File type/resource
GSM688565_BA02_liver_hibernating_N03-056.txt.gz 623.5 Kb (ftp)(http) TXT
Processed data included within Sample table

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