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Sample GSM850463 Query DataSets for GSM850463
Status Public on Oct 02, 2012
Title Smoker 1
Sample type RNA
 
Source name Alveolar macrophages, smoker
Organism Homo sapiens
Characteristics cell type: alveolar macrophages
smoker: yes
pack years: 12
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 6.54848
2672712 6.27603
2842570 6.53113
3526544 4.63163
2902531 5.67453
2402942 6.78039
3382216 6.56382
3771800 7.64854
2427469 4.83454
2392945 6.44725
2453006 5.02107
3552083 5.594
3416651 5.56522
2562821 8.57463
3721851 5.39181
3442176 6.5046
2477438 6.2922
2926969 4.95517
3026969 6.27699
3796335 6.57227

Total number of rows: 22011

Table truncated, full table size 341 Kbytes.




Supplementary file Size Download File type/resource
GSM850463.CEL.gz 21.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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