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Sample GSM464681 Query DataSets for GSM464681
Status Public on Dec 25, 2009
Title B cell smoking-72
Sample type RNA
 
Source name circulating B cells in smoking woman
Organism Homo sapiens
Characteristics age: 59
menopausal: Post
cell type: B cell
smoking: yes
Extracted molecule total RNA
Extraction protocol Seventy milliliters of blood were drawn from each recruited female. B cell isolation from 70 ml whole blood was performed using a positive isolation method with Dynabeads® CD19 (Pan B) and DETACHaBEAD® CD19 (Dynal Biotech, Lake Success, NY, USA) following the manufacturer’s protocols. B cell purity was assessed by flow cytometry (BD Biosciences, San Jose, CA USA) with fluorescence labeled antibodies, PE-CD19 and FITC-CD45. The average purity was 96.3% with less than 1% deviation.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol We use the Affymetrix Microarray Scanner by Hewlett-Packard 2500 and Microarray Suite 5.0 software for chip scanning and raw image generating.
Description Gene expression data from B cells isolated from healthy US white smoking females
Data processing Microarray Suite 5.0 (MAS 5.0, Affymetrix, Santa Clara, CA, USA) software was used to generate array raw data in CEL files. A preselecting procedure adopted by our previous study (Xiao et al. 2008) was also used here. We selected a subset of 7,215 probe sets from a total of 22,283 for ~14,500 genes in the HG-133A array. Subsequent data analyses were performed on these selected probe sets. We applied multiple analytic approaches including mas5.0 algorithm (Affymetrix, Santa Clara, CA, USA), RMA (Robust Multiarray Algorithm), GCRMA (the improved GC-content adjusted RMA), and dChip for converting and normalizing our raw probe data to gene expression values. Genes expressed differentially as determined by consensus using the 4 methods were extracted.
 
Submission date Oct 23, 2009
Last update date Sep 01, 2016
Contact name Feng Pan
E-mail(s) panbaby@gmail.com
Phone 008613601860460
Organization name Xi'an Jiaotong University
Department School of life science and technology
Lab Institute of Genetics
Street address Xian Ning West Road 28
City Xi'an
State/province Shaanxi
ZIP/Postal code 710049
Country China
 
Platform ID GPL96
Series (1)
GSE18723 Gene Expression Circulating B Lymphocytes for Smoking Females
Relations
Reanalyzed by GSE86363

Data table header descriptions
ID_REF
VALUE MAS 5 signal
RMA
GCRMA
dChip

Data table
ID_REF VALUE RMA GCRMA dChip
1007_s_at 619.1643072 7.581324762 6.946935436 1016.12
1053_at 455.6473446 6.412664145 6.331515321 453.64
117_at 378.9806013 6.248376315 3.226510417 309.8
121_at 1028.558554 8.968970053 3.061054317 1049.88
1255_g_at 19.95443835 4.790212308 2.198822587 87.49
1294_at 1027.771454 9.403728989 7.881313217 941.84
1316_at 68.07530309 6.509975761 2.982338214 504.92
1320_at 189.5986418 5.767818292 2.573481106 367.45
1405_i_at 211.1253104 5.736864116 4.336858158 234.65
1431_at 73.19124797 5.040473157 2.687131108 246.83
1438_at 67.96981889 6.611719246 2.181125886 262.77
1487_at 586.1181183 7.025307118 6.001166845 296.92
1494_f_at 373.3880975 6.522292711 2.570284189 236.22
1598_g_at 592.2472886 8.159801521 1.821719945 720.5
160020_at 775.4087786 8.106564042 2.445970955 318.64
1729_at 789.8421665 8.357949058 7.557154725 659.48
177_at 64.97623027 5.504025567 3.00476274 212.66
1773_at 37.90007853 5.444634876 1.983316359 233.85
179_at 770.5308857 9.670874192 1.724441121 1153.22
1861_at 250.0396226 5.416529838 1.950894697 127.94

Total number of rows: 22283

Table truncated, full table size 1164 Kbytes.




Supplementary file Size Download File type/resource
GSM464681_GE-72B.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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