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Sample GSM206286 Query DataSets for GSM206286
Status Public on Dec 30, 2007
Title Chicken liver 6th week Sample 1
Sample type RNA
 
Source name chicken Liver 6 weeks of age
Organism Gallus gallus
Characteristics Breed: Beijing-You chicken
Gender: male
Age: 6 week
Biomaterial provider China Agricultural University
Extracted molecule total RNA
Extraction protocol Tissue samples were ground with pestle in a mortar under liquid nitrogen. Total RNA was extracted by using Trizol reagent from tissue powder, purified by using QIAquick PCR Purification kit.
Label Cy5
Label protocol For fluorescence labeling, 0.5 μl 1 M NaHCO3 and 1 μl Cy3 and Cy5 mono-reactive dyes (Amersham Pharmacia) in DMSO (Sigma) (10 μg/μl) were added to samples, respectively. The reaction mixture was then incubated at 37°C for 2 hours in the dark then purified by QIAquick PCR Purification kit to remove unincorporated fluorophores.
 
Hybridization protocol Two pmoles each of Cy3-labelled or Cy5-labelled sample in hybridization buffer was added to per isolated sub-array.
cover the droplet with tiny cover slips with forceps, place the slide in a hybridization cassette and incubate the cassette for 16h at 42°C.
washed in 2X SSC and 0.1% SDS (5 min, 55°C), 1X SSC and 0.1% SDS (5 min, 55°C), 0.1 X SSC (30sec, 3 X), and dried by centrifugation.
Scan protocol Fluorescent array images were collected individually in each sub-array area for Cy3 or Cy5 in a GenePix 4000B fluorescent scanner (Axon Instruments, CA)
Description Indigenous chicken liver samples hybridized with samll group of genes which related to lipid metabolism.
Data processing Based onhousekeeping genes that are relatively invariant for printed cDNA microarry as positive control, an edited normalization method using Fortran software was used for for all data processing
 
Submission date Jun 28, 2007
Last update date Aug 14, 2011
Contact name Huifeng Li
E-mail(s) lihuifengtom@yahoo.com.cn
Phone 1-540-231-3183
Fax 1-540-231-3010
Organization name Virginia Tech
Department Animal and Poultry Sciences
Lab Biotechnology
Street address 3570 Litton Reaves Hall
City Blacksburg
State/province VA
ZIP/Postal code 24061-0306
Country USA
 
Platform ID GPL5442
Series (1)
GSE8405 A new multi-sample hybridized microarray platform for quantitative gene expression on a small scale

Data table header descriptions
ID_REF
SIGNAL_RAW Raw signal data from Cy3 or Cy5
BKD_RAW Background data
VALUE SIGNAL_RAW-BKD_RAW

Data table
ID_REF SIGNAL_RAW BKD_RAW VALUE
1 3895 3510 385
2 4618 4489 129
3 4320 4394 -74
4 5024 4559 465
5 6494 4625 1869
6 6236 4484 1752
7 49953 4048 45905
8 49382 3001 46381
9 9448 4057 5391
10 12420 4517 7903
11 7943 4374 3569
12 7477 4601 2876
13 4720 4688 32
14 4333 4550 -217
15 5111 4434 677
16 4030 3358 672
17 6971 4227 2744
18 7169 4381 2788
19 15482 4420 11062
20 14038 4490 9548

Total number of rows: 64

Table truncated, full table size 1 Kbytes.




Supplementary file Size Download File type/resource
GSM206286.txt.gz 7.6 Kb (ftp)(http) TXT
Raw data included within Sample table
Processed data provided as supplementary file

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