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Sample GSM2210943 Query DataSets for GSM2210943
Status Public on Sep 09, 2016
Title Nrf2 null whole lung SP rep1
Sample type RNA
 
Source name Whole lung tissue from Nrf2 null (Nfe2l2 -/-) mice given S. pneumoniae
Organism Mus musculus
Characteristics tissue: Whole lung
background strain: C57BL/6
genotype: Nrf2 null (Nfe2l2 -/-)
age: 6-12 weeks
inoculation agent: Streptococcus pneumoniae
Treatment protocol Anesthetized mice received PBS or a suspension containing S. pneumoniae instilled intratracheally into the left lung at a dose of 2.3 µl/g mouse body weight.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from mouse lungs using miRNeasy kits from Qiagen (Valencia, CA, USA) according to the manufacturer's instructions.
Label biotin
Label protocol Total RNA (250 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridize onto Affymetrx arrays. 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 Affymtrix peg plate arrays was carried out using the Affymetrin GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.
Description Gene expression data from mouse lung
Data processing Affymetrix Expression Console Software was used for basic data analysis and quality control. Microarray data were preprocessed by RMA (Robust Multiarray Average) background correction, GC content and sequence correction, quantile normalization, and median polish summarization, and expression levels compared using ANOVA on log2 intensities to identify transcripts that were differentially expressed between genotype and treatment groups. Differentially expressed (DE) mRNAs were filtered at Benjamini-Hochberg FDR < 0.05, and fold change > 2, and expression patterns of DE transcripts were visualized using hierarchical clustering. Expression analyses were performed using Partek Genomics Suite (Partek Inc., St. Louis. MO, USA). Gene Set Enrichment Analysis (GSEA) was performed according to the method described (12, 13). In addition to gene sets derived from Gene Ontology (GO) biological processes, GSEA for Nrf2 regulated genes was performed using lists of Nrf2 regulated genes from the literature (14, 15).
The .mps file used in this analysis is available on the Superseries record.
 
Submission date Jun 22, 2016
Last update date Sep 09, 2016
Contact name Claire M. Doerschuk
Organization name University of North Carolina at Chapel Hill
Department Marsico Lung Institute
Street address Marsico Hall 7205 CB#7248
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7248
Country USA
 
Platform ID GPL22070
Series (2)
GSE83612 Gene expression profiling of neutrophils and whole lung tissue from wildtype and Nrf2 null (Nfe2l2-/-) mice during S. pneumoniae pneumonia [whole lung]
GSE83615 Gene expression profiling of neutrophils and whole lung tissue from wildtype and Nrf2 null (Nfe2l2-/-) mice during S. pneumoniae pneumonia

Data table header descriptions
ID_REF
VALUE RMA log2

Data table
ID_REF VALUE
AB618486 3.91147
AF067064 4.58848
AF075717 4.98992
AF143094 7.50437
AF248058 10.2757
AF285583 4.4018
AF295105 8.03743
AF358728 4.11075
AF394949 5.38397
AF469169 7.89765
AJ237586 4.02819
AJ459773 6.97754
AK002956 11.0114
AK003851 3.78643
AK005807 3.99014
AK005827 4.23938
AK006077 3.82594
AK006189 3.96014
AK006298 7.25353
AK006338 5.01274

Total number of rows: 31350

Table truncated, full table size 637 Kbytes.




Supplementary file Size Download File type/resource
GSM2210943_A7.CEL.gz 5.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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