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Sample GSM464721 Query DataSets for GSM464721
Status Public on Dec 25, 2009
Title B cell nonsmoking-39B
Sample type RNA
 
Source name circulating B cells in non-smoking woman
Organism Homo sapiens
Characteristics age: 44
menopausal: Pre
cell type: B cell
smoking: no
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 non-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 638.0677649 7.714484473 7.073646142 939.33
1053_at 511.8980737 6.662270239 6.501983817 357.33
117_at 86.69190022 5.976045161 3.123773878 249.65
121_at 976.4422144 8.846408003 3.131515247 989.01
1255_g_at 113.5979029 4.88288692 2.223454719 87.18
1294_at 926.7435994 8.948709931 7.547166553 688.59
1316_at 128.429759 6.570828386 2.989618667 492.12
1320_at 226.9353369 5.791659122 2.588949004 233.34
1405_i_at 20.86084542 5.514552934 3.918669272 182.08
1431_at 127.2198325 5.086085993 2.742617479 203.42
1438_at 48.72210586 6.506088639 2.161634094 232.62
1487_at 365.0011137 6.603638776 5.722835027 232.01
1494_f_at 315.7089089 6.521515186 2.625061399 277.78
1598_g_at 657.5416765 8.114344549 1.825389438 624.43
160020_at 889.4159602 8.084285945 2.663185512 302.52
1729_at 822.4098911 8.192744521 7.524701679 713.41
177_at 146.9712995 5.387680541 3.016539389 224.43
1773_at 229.2293497 5.658014995 1.968692014 284.42
179_at 740.3891656 9.005829171 1.713942776 919.6
1861_at 196.3253759 5.481392776 1.9465107 146.09

Total number of rows: 22283

Table truncated, full table size 1164 Kbytes.




Supplementary file Size Download File type/resource
GSM464721_GE-39B2.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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