NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2580059 Query DataSets for GSM2580059
Status Public on Jun 01, 2018
Title Venous blood_D95_P_W702
Sample type RNA
 
Source name Venous blood, 95 days, progressive, foal W702
Organism Equus caballus
Characteristics breed: Welsh Pony
tissue: whole blood
developmental stage: foal
gender: female
weening type: progressive
time after weaning: 95 days
horse id: W702
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 progressive 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 21.28986275
6 23.28361988
8 29.31949545
9 35.33581574
11 25.51507359
12 14.53934513
13 29.58315482
16 37.19149995
17 34.94926145
18 15.96972199
19 31.91659454
20 42.97980323
21 31.70344819
22 32.3669012
23 48.24935734
25 18.78818399
27 41.75957054
29 13.17122888
30 28.31734895
32 28.73384765

Total number of rows: 26534

Table truncated, full table size 457 Kbytes.




Supplementary file Size Download File type/resource
GSM2580059_US10463851_258142110003_S01_GE1_1010_Sep10_1_2.txt.gz 11.9 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap