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Sample GSM895941 Query DataSets for GSM895941
Status Public on Mar 13, 2015
Title Female Qingyuan partridge Chicken DNA vs female Dehong DNA
Sample type genomic
 
Channel 1
Source name Female Qingyuan partridge Chicken blood
Organism Gallus gallus
Characteristics tissue: blood
age: adult
gender: Female
breed: Qingyuan partridge
Treatment protocol Blood sample were got from adult chicken individuals by syringe and kept in 0.5M EDTA solution in order to avoid error.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using DNeasy Blood & Tissue kit(QIAGEN No.69504) and Wizard Genomic DNA purification kit(Promega No.A1125) by the standard protocal for each kit separately.
Label cy5
Label protocol 1.5µg of genomic DNA was digested with restriction enzymes AluI and RsaI and fluorescently labelled using the Agilent Genomic DNA Labeling Kit PLUS (Agilent technologies).Test samples were labelled with cyanine 5-dUTP and the reference sample with cyanine 3-dUTP.
 
Channel 2
Source name Dehong chicken
Organism Gallus gallus
Characteristics tissue: blood
age: adult
breed: Dehong
gender: female
Treatment protocol Blood sample were got from adult chicken individuals by syringe and kept in 0.5M EDTA solution in order to avoid error.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using DNeasy Blood & Tissue kit(QIAGEN No.69504) and Wizard Genomic DNA purification kit(Promega No.A1125) by the standard protocal for each kit separately.
Label cy3
Label protocol 1.5µg of genomic DNA was digested with restriction enzymes AluI and RsaI and fluorescently labelled using the Agilent Genomic DNA Labeling Kit PLUS (Agilent technologies).Test samples were labelled with cyanine 5-dUTP and the reference sample with cyanine 3-dUTP.
 
 
Hybridization protocol Array hybridization was performed using Agilent Oligo aCGH Hybridization Kit (Agilent technologies) for 40 h at 20 rpm in a 65℃ Agilent hybridization oven.
Scan protocol Arrays were scanned at 3μm resolution using an Agilent Microarray Scanner, and image analysis was performed using Feature Extraction software 10.7 with 90% laser power value and PMT 100%.
Description Female Qingyuan partridge Chicken DNA sample vs Dehong chicken DNA sample.DNA were collected from chicken blood with 0.5 M EDTA and stored at -20°C until DNA isolation.
Data processing Agilent Feature Extraction Software 10.7 was used for background subtraction and LOWESS normalization.
 
Submission date Mar 14, 2012
Last update date Mar 13, 2015
Contact name ming tian
E-mail(s) mingtian830618@gmail.com
Phone +86 15001088986
Organization name China Agricultural University
Street address No.2, Yuan Ming Yuan West Road, Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100193
Country China
 
Platform ID GPL13398
Series (1)
GSE36504 Dehong chicken blood samples vs. 22 different chicken blood samples belonging to 11 breeds

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 1.072957174e-001
2 0.000000000e+000
3 0.000000000e+000
4 4.326831049e-002
5 -5.830481382e-002
6 1.534825129e-002
7 -7.510823358e-002
8 -7.383362069e-002
9 7.571565114e-002
10 -5.754055366e-002
11 -4.995650558e-002
12 1.349018185e-002
13 3.555861875e-002
14 5.170419639e-002
15 -7.987562910e-002
16 -2.144434863e-001
17 -7.498964651e-002
18 -3.458208433e-002
19 -8.478096871e-002
20 2.148908991e-002

Total number of rows: 420288

Table truncated, full table size 9937 Kbytes.




Supplementary file Size Download File type/resource
GSM895941_253111210010_S01_CGH_107_Sep09_1_1.txt.gz 43.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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