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Sample GSM8186276 Query DataSets for GSM8186276
Status Public on Apr 08, 2024
Title Lung of rat exposed to 21% oxygen at 0 ft for 5 h, biological rep1
Sample type RNA
 
Source name Lung
Organism Rattus norvegicus
Characteristics tissue: Lung
Treatment protocol Heart, lung, and hippocampus samples were placed on dry ice immediately. Blood was collected in PAXgene blood RNA stabilization tubes and frozen. Solid tissues were placed in RNAlater ICE before processing.
Growth protocol Rats were subjected to different levels of hypobaria and/or hyperoxia for different durations of time at room temp. Immediately after "flight", rats were anesthetized and euthanized and tissue was collected.
Extracted molecule total RNA
Extraction protocol All tissues were processed for RNA via commercially available and appropriate kits (trizol for solid tissue, PAXgene kit for blood).
Label Biotin
Label protocol 150 ng RNA was transcribed to double-stranded cDNA, followed by synthesis and purification of cRNA. 2nd-cycle ss-cDNA was then synthesized and then purified after RNA hydrolysis using RNase H.
 
Hybridization protocol ss-cDNA was fragmented and labeled before hybridization onto the microarray chips, which were washed and processed using an Affymetrix GeneChip system 3000 7G.
Scan protocol Affymetrix image data (.CEL files) was further analyzed using the R statistical analysis tool. The R ‘oligo' package was used to access the intensity values which were normalized using the ‘Robust Multichip Average (RMA)’ normalization method provided by the R ’limma’ package.
Description These were the control group animals, therefore they were used as reference for differential expression of the treated groups and do not have a separate processed data file.
Data processing The samples were assessed and corrected for any batch effects before downstream analyses. Principal component analysis was utilized to identify and exclude any outlier samples. A general linear model was utilized to fit the expression values for each gene.
TXT files are available along with the CEL files. TXT files compared treatment groups to the control group after outliers were removed. The list of .TXT files and associated .CEL files are found on the Matrix table. We used the analyzed data within TXT files for our results and conclusions.
 
Submission date Apr 03, 2024
Last update date Apr 08, 2024
Contact name Apurva Borcar
E-mail(s) aborcar@som.umaryland.edu
Organization name University of Maryland School of Medicine
Department Anesthesiology
Lab Fiskum
Street address 685 W. Baltimore Street, MSTF 5-34
City Baltimore
State/province MD
ZIP/Postal code 21201
Country USA
 
Platform ID GPL23040
Series (1)
GSE263131 Acute Changes in Rat Tissue Gene Expression Following Exposure to Flight Relevant Hypobaria

Supplementary file Size Download File type/resource
GSM8186276_Fiskum_RatClariomS_Run4-5-GH05-LNG.CEL.gz 1.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data are available on Series record

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