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Sample GSM470017 Query DataSets for GSM470017
Status Public on Nov 13, 2009
Title Pooled retinal RNA from cyclic hyperoxia-exposed post-natal day 3 F344 rats, biological replicate 1
Sample type RNA
 
Source name Retinae, exposed to cyclic hyperoxia to post-natal day 3
Organism Rattus norvegicus
Characteristics strain: Fischer 344
Treatment protocol Within 12 hours of birth, female rats and their litters were placed in a humidified oxygen chamber and exposed to alternating 24 hour cycles of hyperoxia (80% oxygen in air) and normoxia (21% oxygen in air) until the rats were euthansed at post-natal day 3. Age-matched room air-exposed rats were used as controls.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the retinae of individual rats using TRIzol according to the manufacturer's method. Total RNA was further purified using a Qiagen Rneasy Micro column purification kit according to the manufacturer's protocol.
Label Biotin
Label protocol As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix WT cDNA Synthesis and Amplification Kit (Part# 900673) and Affymetrix WT Terminal Labeling and Control Regents (Part# 901524). The rRNA reduction step is not recommended by Affymetrix for the Genearrays and was not performed.
 
Hybridization protocol As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix Genechip Hybridization, Wash and Stain Kit (P/N 900720)
Scan protocol As per Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual (P/N 701880 Rev4) using Affymetrix Genechip Scanner 3000 7G
Description Gene Expression Data
Data processing CEL files generated from DAT files automatically by Affymetrix AGCC software. CEL files processed using Partek Genomics Suite v 6.4 using RMA background correction and Partek GC content correction.
 
Submission date Nov 12, 2009
Last update date Nov 12, 2009
Contact name Melinda N Tea
E-mail(s) melinda.tea@flinders.edu.au
Organization name Flinders University
Department Ophthalmology
Lab Rm 5D214
Street address Flinders Medical Centre, Carpark Building
City Adelaide
State/province South Australia
ZIP/Postal code 5042
Country Australia
 
Platform ID GPL6247
Series (1)
GSE18998 Gene expression microarray analysis of early oxygen-induced retinopathy (OIR)

Data table header descriptions
ID_REF
VALUE Processed, Log2 transformed, intensities from Partek Genomics Suite v6.4

Data table
ID_REF VALUE
10701620 4.9
10701630 4.3
10701632 4.4
10701636 4.4
10701643 4.9
10701648 4.8
10701654 4.7
10701663 6.5
10701666 5.5
10701668 5.3
10701671 4.5
10701674 5.0
10701679 4.6
10701684 5.0
10701689 7.6
10701691 4.8
10701697 6.4
10701699 8.7
10701709 10.3
10701714 4.9

Total number of rows: 27342

Table truncated, full table size 348 Kbytes.




Supplementary file Size Download File type/resource
GSM470017.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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