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Sample GSM2865405 Query DataSets for GSM2865405
Status Public on May 01, 2018
Title non_WB_but_severe_WS_rep4
Sample type RNA
 
Source name Breast meat with severe white striping defect but without wooden breast defect, ≤45 days, replicate 4
Organism Gallus gallus
Characteristics tissue: chicken breast muscle
wooden breast defect: no
white striping defect: severe
age: 45 days or under
gender: male
Treatment protocol Breast meat samples were classified as “non-defect”, “WS” or “WB” based on their appearance. The defective samples were further classified based on different defect severity. For WS, there were 3 severity levels, i.e. mild, moderate and severe. For WB, 2 severity levels, moderate and severe, were classified.
Growth protocol Commercial broilers (ROSS) were raised under a uniform industrial standard practice at five different farms located around the central of Thailand. When reach the desirable slaughter age, the birds were transferred to an industrial abattoir located in Saraburi province (Thailand) and harvested according to a standard industry practice. The pectoralis major muscle from one side of the breasts was collected and snap frozen in liquid nitrogen and stored at -80C until RNA isolation.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from chicken muscle samples using TRIzolTM Reagent (Invitrogen) according to the manufacturer’s instruction. The isolated RNA was precipitated by mixing 500 μL of the aqueous phase with an equal volume of isopropanol. The pellet of the total RNA was collected by centrifugation and subsequently resuspended using sterile deionized water. Quantity and integrity of total RNA was determined using a Nanodrop and Bioanalyzer, respectively. The RNA samples with RIN exceed 7.0 were used in this study.
Label Cy3
Label protocol A total of 40 arrays (8 slides) were hybridized in this project. One hundred nanograms of total RNA was labeled using One-color Low Input Quick Amp Labeling Kit (Agilent) the manufacturer's recommendations. In brief, total RNA was reverse transcribed into double-stranded cDNA by priming with Oligo(dT) primer. The synthesized cDNA was subjected to an In vitro transcription using T7 RNA polymerases to produce cyanine 3CTP labeled complementary RNA (cRNA). The cRNA was purified using Qiagen RNeasy kit (Qiagen) and quantified using Nanodrop.
 
Hybridization protocol 600 ng purified cRNA was hybridized onto the Aglient SurePrint array at 65°C for 17 h. The array was subsequently washed for 1 min at room temperature in Gene Expression Washing buffer I (Agilent), followed by another minute at 37°C in Washing buffer II (Agilent).
Scan protocol The array was gently blotted dry using Kimwipe® and scanned using Agilent High Resolution Microarray Scanner (C Model, Agilent).
Description Gene expression of breast meat that showed severe white striping defect and without wooden breast defect
Data processing The scan image were analyzed by Agilent Feature Extraction Software version V10.7.1.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. If the signal intensities were flaged as not-detected and data were missed across arrays more than 50% of total arrays within group, that probes were discarded from analysis.
 
Submission date Nov 27, 2017
Last update date May 01, 2018
Contact name Yuwares Malila
Organization name National Center for Genetic Engineering and Biotechnology
Street address 113 Thailand Science Park Phahonyothin Road Khlong Nueng, Khlong Luang
City Pathumthani
ZIP/Postal code 12120
Country Thailand
 
Platform ID GPL24307
Series (1)
GSE107362 Phenotypic and genotypic relationships between meat quality characteristics and expression of target genes associated with broiler meat quality defects

Data table header descriptions
ID_REF
VALUE Normalized signal intensity. Wooden breast data was normalized by quantile normalization. White striping data was normalized by quantile normalization and then combat normalization.

Data table
ID_REF VALUE
1
2
3
4
5 103.62701
6
7 214.77548
8 313.68005
9 158.34538
10 2321.7593
11 736.5483
12
13
14
15 404.3955
16 283.04376
17 7383.729
18 2142.622
19
20 656.7804

Total number of rows: 62976

Table truncated, full table size 765 Kbytes.




Supplementary file Size Download File type/resource
GSM2865405_US83503546_258479210012_S01_GE1_107_Sep09_2_3.txt.gz 3.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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