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Sample GSM2580061 Query DataSets for GSM2580061
Status Public on Jun 01, 2018
Title Venous blood_D95_B_W708
Sample type RNA
 
Source name Venous blood, 95 days, brutal, foal W708
Organism Equus caballus
Characteristics breed: Welsh Pony
tissue: whole blood
developmental stage: foal
gender: female
weening type: brutal
time after weaning: 95 days
horse id: W708
Treatment protocol 5ml venous blood were collected from the 32 foals, 30 and 95 days after weaning, using vacuum tubes which included a reagent that immediately stabilized intracellular RNA (PAXgene blood RNA system, PreAnalytiX GmbH, Hombrechtikon, Switzerland). The samples were kept at room temperature for 8 h as required for stabilizing RNA and then at -20°C until RNA extraction.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the PAXgene Blood RNA kit (Qiagen, Courtaboeuf, France) according to the manufacturer's protocol. Total RNA quality was assessed and its concentration was measured using RNA Nano chips onto a Bioanalyser 2100 (Agilent, Boeblingen, Germany).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of DNase pre-treated (0.2μl DNase 10X, 0.4μl 10X Buffer DNase, 0.4μl RNasin 40U/μl, 3μl total RNA) total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNA clean-up using Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).
 
Hybridization protocol 600 ng of Cy3-labelled cRNA were hybridized on the microarray slides following the manufacturer’s instructions.
Scan protocol Immediately after washing, the slides were scanned on Agilent G2505C Microarray Scanner using Agilent Scan Control A.8.5.1 software.
Description Gene expression 95 days after brutal weaning in foal blood.
Data processing The fluorescence signal was extracted using Agilent Feature Extraction software v10.10.1.1 with default parameters.
Raw data (median of pixels intensity) were filtered, log2 transformed, corrected for batch effects (washing and labeling serials) and normalized using quantile method.
 
Submission date Apr 17, 2017
Last update date Feb 10, 2019
Contact name Aline FOURY
E-mail(s) aline.foury@inrae.fr
Organization name INRAE
Lab NutriNeuro
Street address 146 rue Léo Saignat
City Bordeaux
ZIP/Postal code 33600
Country France
 
Platform ID GPL23307
Series (2)
GSE97906 Effect of a progressive weaning on behavioural and physiologic indicators in foals (Equus caballus)
GSE97908 Effect of a progressive weaning on behavioural and physiologic indicators in foals and mares (Equus caballus)

Data table header descriptions
ID_REF
VALUE Normalized log2 signal intensity

Data table
ID_REF VALUE
5 21.27368762
6 24.0601824
8 29.78764322
9 36.64279242
11 25.51274715
12 14.55709547
13 30.48917904
16 36.77169226
17 34.94887586
18 16.50434386
19 32.19214594
20 42.79707505
21 32.72363686
22 31.21562162
23 49.60603423
25 17.9386262
27 40.60024966
29 13.22487998
30 28.60065866
32 28.3887196

Total number of rows: 26534

Table truncated, full table size 457 Kbytes.




Supplementary file Size Download File type/resource
GSM2580061_US10463851_258142110003_S01_GE1_1010_Sep10_1_4.txt.gz 11.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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