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Sample GSM2580047 Query DataSets for GSM2580047
Status Public on Jun 01, 2018
Title Venous blood_D95_B_MW544
Sample type RNA
 
Source name Venous blood, 95 days, brutal, foal MW544
Organism Equus caballus
Characteristics breed: Welsh Pony
tissue: whole blood
developmental stage: foal
gender: male
weening type: brutal
time after weaning: 95 days
horse id: MW544
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 21.13117264
6 24.42435169
8 29.58205214
9 34.82318292
11 25.71092652
12 14.62516465
13 29.75893242
16 36.30819934
17 35.53403696
18 16.06688877
19 31.83643805
20 42.23297107
21 32.37526767
22 33.13814264
23 48.5791546
25 18.93715738
27 40.05656887
29 12.52633465
30 27.75263546
32 28.53233824

Total number of rows: 26534

Table truncated, full table size 457 Kbytes.




Supplementary file Size Download File type/resource
GSM2580047_US10463851_258142110001_S01_GE1_1010_Sep10_2_2.txt.gz 11.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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