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Sample GSM2967138 Query DataSets for GSM2967138
Status Public on Mar 18, 2019
Title WT_Smoke_Female_5day_Rep3
Sample type RNA
 
Source name RNA isolated from whole lung tissue from female BENaC mice given 5 days of smoke exposure
Organism Mus musculus
Characteristics tissue: Homogenized whole lung tissue
genotype: Wildtype (WT)
exposure: Smoke
Sex: Female
exposure duration: 5 day
Treatment protocol Sex-matched 5-7-week old WT and βENaC littermates were exposed to cigarette smoke or sham (room air) exposure. Each exposure and genotype group included both males and females (n=5 animals of each sex per group for most groups. In the 5-day female group, there were n=6 WT sham animals and n=4 βENaC sham animals). Exposure occurred in a plexiglass chamber attached to a smoke delivery device using an exposure chamber and smoking machine (inExpose Exposure System, SCIREQ, Chandler, AZ). The chamber contained pie-slice separators and positions for 16 mice. Mice were exposed to mainstream + side-stream smoke from 6 reference cigarettes with filters removed per day (College of Agriculture Reference Cigarette Program, University of Kentucky, 3R4F research cigarettes) [18]. Each cigarette was puffed for 2 sec every 25 sec, using the standard Federal Trade Commission smoking machine protocol [18]. The sham-exposed control mice were exposed to room air in the exposure chamber for a time equivalent to that needed for active smoke exposure. Mice were exposed to cigarette or sham smoke for 1 day or 5 consecutive days. Samples were harvested 4 hours after the completion of the final smoke exposure. The right lung was used for gene expression analysis.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using miRNeasy kits from Qiagen (Valencia, CA, USA) according to the manufacturer's instructions. RNA was isolated from lung tissue homogenates using the miRNeasy kit (Qiagen). Spectrophotometric ratios of A260/A280 and A260/A230 were 1.7-2.1 and greater than 1.6, respectively. RIN values were greater than 7.4; the average RIN for all samples was 9.1.
Label biotin
Label protocol Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridize onto Affymetrx arrays. All 80 samples were run on the same 96 well array plate. The Affymetrix HT WT User Manual was followed to prepare the samples. Briefly, the WT Expression HT Kit for Robotics (Ambion) was used to generate sense-strand cDNA from total RNA. Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip HT Terminal Labeling Kit. The Beckman Coulter Biomek FXP Laboratory Automation Workstation with the Target Express set up was used to prepare the samples with these two kits.
 
Hybridization protocol Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays. Hybridization, washing, staining and scanning of the Affymtrix peg plate arrays was carried out using the Affymetrin GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.
Scan protocol Scanning of the Affymetrix peg plate arrays was carried out using the Affymetrix GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.
Data processing Data were evaluated using Affymetrix Expression Console v1.4 software for quality control based on summary statistics, and Partek Genomics Suite v6.6 for normalization. Expression signals from CEL files were preprocessed and normalized by RMA (Robust Multiarray Average) background correction, GC content and probe sequence correction, quantile normalization, and median polish summarization of probe signals mapped to specific genes. Custom probeset-to-gene mappings were generated from Affymetrix Probeset and Transcript Annotation release 35 by consolidating all probesets mapped, in order of preference, to Ensembl 81 gene ID, Refseq mRNA, and Genbank accession numbers. The RMA-normalized log2 intensity values were used as input for the General Linear Model (glm) function in R.
 
Submission date Jan 29, 2018
Last update date Mar 18, 2019
Contact name Claire M Doerschuk
Organization name UNC Chapel Hill
Street address 125 Mason Farm Rd. CB#7248
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL22070
Series (1)
GSE109776 Gene expression after 1 and 5 days of cigarette smoke exposure in mice with chronically inflamed or healthy lungs

Data table header descriptions
ID_REF
VALUE RMA log2

Data table
ID_REF VALUE
NM_001166372 5.9479
NM_001290273 3.0514
NM_145486 8.14736
XM_006497194 7.793
NM_177115 5.91687
NM_001045533 5.72506
NM_027314 8.83995
NM_172606 9.43619
NM_020575 8.63229
NM_027920 7.87735
NM_001033262 4.36222
NM_001039242 3.12792
NM_177597 2.77618
NM_017461 6.94295
NM_001159717 9.5937
XM_006520992 5.45198
NM_001284392 6.29223
NM_001253706 6.59704
NM_001205367 10.2583
NM_001252332 7.32577

Total number of rows: 31350

Table truncated, full table size 637 Kbytes.




Supplementary file Size Download File type/resource
GSM2967138_12272.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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