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Sample GSM850459 Query DataSets for GSM850459
Status Public on Oct 02, 2012
Title Non-smoker 1
Sample type RNA
 
Source name Alveolar macrophages, non-smoker
Organism Homo sapiens
Characteristics cell type: alveolar macrophages
smoker: no
Treatment protocol None
Growth protocol None
Extracted molecule total RNA
Extraction protocol RNA was isolated from alveolar macrophages using the MirVana (Applied Biosystems (ABI), Austin, TX) reagents according to the manufacturer's instructions.
Label biotin
Label protocol Microarray hybridizations were performed at the University of Iowa DNA Facility. Briefly, 25 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN. Four ug of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above. Five micrograms of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.
 
Hybridization protocol Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Exon 1.0 ST arrays (Part No. 900650), and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 GeneChip Hybridization Oven. Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), and signal amplified with anti-streptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.
Scan protocol Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade, and data were collected using the GeneChip Operating Software (GCOS) v1.4.
Data processing CEL files were imported into PartekGS version 6.5 and normalized using the standard RMA workflow. The gene values were obtained using mean value summarization.

Genome build: hg18
Exons used in analysis: core
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
 
Submission date Dec 16, 2011
Last update date Oct 02, 2012
Contact name Thomas B Bair
E-mail(s) iihg-bioinformatics@uiowa.edu
Organization name University of Iowa
Street address 335 EMRB
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
 
Platform ID GPL5175
Series (1)
GSE34517 Cigarette smoking alters mRNA expression in human alveolar macrophages

Data table header descriptions
ID_REF
VALUE RMA-normalized log2 values from PartekGS

Data table
ID_REF VALUE
3881686 6.3715
2672712 6.30108
2842570 6.59979
3526544 4.73585
2902531 5.55146
2402942 7.00817
3382216 6.89685
3771800 7.69267
2427469 4.65958
2392945 6.26991
2453006 5.67304
3552083 5.46062
3416651 5.52725
2562821 8.49284
3721851 5.40716
3442176 6.56801
2477438 5.56444
2926969 6.17633
3026969 6.23088
3796335 6.45292

Total number of rows: 22011

Table truncated, full table size 341 Kbytes.




Supplementary file Size Download File type/resource
GSM850459.CEL.gz 23.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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