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Sample GSM1527040 Query DataSets for GSM1527040
Status Public on Oct 17, 2014
Title CB 7th day embryo_sample 2
Sample type RNA
 
Source name 7th day embryo of control broiler bird
Organism Gallus gallus
Characteristics breed: broiler
tissue: whole embryo
developmental stage: 7th day embryo
Treatment protocol Embryo of Aseel bird was used as treatment group and embryo of broiler bird was used as control group. Aseel was slow-growing bird while control broiler was fast-growing line.
Growth protocol Chickens were reared following standard managemental protocol at the Institute farm from where fertile eggs were collected. The fertile eggs were kept in the Institute hatchery for embryonic development.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIZOL method. Total RNA and cRNA Purification Kit: Qiagen’s RNeasy Mini Kit (Cat#74104) was used.
Label Cy3
Label protocol The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double-stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis, Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated were determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.
 
Hybridization protocol 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).
Scan protocol Scanned using Agilent Technologies G2505C scanner.
Description Gene expression at embryonic stage.
Data processing Images were quantified using Feature Extraction Software (Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.
 
Submission date Oct 16, 2014
Last update date Oct 17, 2014
Contact name Tarun K Bhattacharya
E-mail(s) bhattacharyatk@gmail.com
Organization name Directorate of Poultry Research
Lab Molecular Genetics and Breeding
Street address Rajendranagar
City Hyderabad
ZIP/Postal code 500030
Country India
 
Platform ID GPL19304
Series (2)
GSE62443 Fold change of expression in Aseel (an indigenous chicken breed) as compared to broiler chicken in 7th day of embryonic stage
GSE62445 Expression in Aseel (an indigenous chicken breed) as compared to broiler chicken in 7th and 18th days of embryonic stage

Data table header descriptions
ID_REF
VALUE Log base 2 normalized signal intensity

Data table
ID_REF VALUE
GT_EA606_A_87_P021623 -5.58
GT_EA606_A_87_P178783 -5.77
GT_EA606_A_87_P227173 -0.48
GT_Chicken_Sp_CO762417_7848 -2.24
GT_EA606_A_87_P068106 -6.83
GT_EA606_A_87_P036534 -2.02
GT_EA606_A_87_P055181 2.95
GT_Chicken_Sp_CN222550_3562 -7.34
GT_EA606_A_87_P011462 -1.94
GT_EA606_A_87_P015165 -2.67
GT_EA606_A_87_P009992 -4.85
GT_EA606_A_87_P018629 -2.16
GT_EA606_A_87_P050426 3.39
GT_EA606_A_87_P036576 -2.76
GT_EA606_A_87_P306948 -1.29
GT_EA606_A_87_P018480 1.58
GT_EA606_A_87_P070546 -7.32
GT_EA606_A_87_P011182 -1.54
GT_EA606_A_87_P052131 7.52
GT_EA606_A_87_P073336 -1.71

Total number of rows: 57149

Table truncated, full table size 1635 Kbytes.




Supplementary file Size Download File type/resource
GSM1527040_US90403632_254267510001_S01_GE1_107_Sep09_1_2.txt.gz 11.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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