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Sample GSM1209689 Query DataSets for GSM1209689
Status Public on Aug 15, 2013
Title Fetus from pregnant ewe exposed to 110 days of hypoxia at high altitude 4
Sample type RNA
 
Source name Carotid Arteries, hypoxia
Organism Ovis aries
Characteristics maternal treatment: hypoxia
gestation: 140d
tissue: fetal carotid arteries
Treatment protocol For the hypoxia study, at 30 days gestation, ewes were transported to the Barcroft Laboratory, White Mountain Research Station (WMRS, CA; elevation 3,801 m, barometric pressure -480 Torr), where they were kept until 135 days gestation. They were maintained in an sheltered outdoor pen that was sheltered and were fed with alfalfa pellets ad libitum. Sheep in both groups were kept in natural day-night conditions.
For control (normoxic) group, sheep were maintained at the suppliers ranch (a 300 m elevation) on alfalfa pellets ad libitum.
Extracted molecule total RNA
Extraction protocol Tissue samples were lysed in Tri-reagent (Ambion, Austin, TX) and total RNA was isolated using phenol/chloroform extraction, followed by purification over spin columns (Ambion). The concentration and purity of total RNA was measured by spectrophotometry at OD260/280, and the quality of the total RNA sample was assessed using an Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies).
Label cy3
Label protocol Labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, 1 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase. The quantity and quality of the labeled cRNA was assayed by spectrophotometry and the Agilent Bioanalyzer.
 
Hybridization protocol One µg of purified cRNA was fragmented to uniform size and applied to Agilent Sheep Gene Expression Microarray, 8 x 15K (Design ID 019921, Agilent Technologies) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a shaking incubator and washed at 37° C for 1 min.
Scan protocol Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies) at 5 µm resolution.
Description Transcriptome analysis
Data processing Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with Gene Spring GX v7.3.1 software (Agilent Technologies). Annotations are based on the Agilent eArray annotation file dated January, 2010.
 
Submission date Aug 15, 2013
Last update date Aug 15, 2013
Contact name Ravi Goyal
E-mail(s) rgoyal@live.com
Phone 9092531596
Organization name University of Arizona
Street address PO Box 64682
City TUCSON
State/province Arizona
ZIP/Postal code 85728
Country USA
 
Platform ID GPL10778
Series (1)
GSE49920 Antenatal maternal long-term hypoxia: acclimatization responses with altered gene expression in ovine fetal carotid arteries

Data table header descriptions
ID_REF
VALUE Normalized Signal Intensity

Data table
ID_REF VALUE
A_70_P012986 0.117
A_70_P024431 0.010
A_70_P065331 0.812
A_70_P065336 0.755
A_70_P061576 0.281
A_70_P061581 0.010
A_70_P061586 0.884
A_70_P061591 0.049
A_70_P061596 0.010
A_70_P061601 0.020
A_70_P026676 0.010
A_70_P026677 0.010
A_70_P061611 0.211
A_70_P061616 0.010
A_70_P061621 0.010
A_70_P061636 0.010
A_70_P061641 2.467
A_70_P061646 4.336
A_70_P061651 0.570
A_70_P012541 368.169

Total number of rows: 15008

Table truncated, full table size 279 Kbytes.




Supplementary file Size Download File type/resource
GSM1209689_FH4.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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