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Sample GSM190747 Query DataSets for GSM190747
Status Public on May 20, 2008
Title Human Saliva Male 4
Sample type RNA
 
Source name Healthy male
Organism Homo sapiens
Characteristics saliva supernatant
male
Growth protocol Whole saliva was collected by direct spitting into 50ml Falcon tubes placed on ice. Supernatant was obtained following centrifugation of whole saliva for 15 minutes at 2600 g.
Extracted molecule total RNA
Extraction protocol RNA was isolated from 560 µL of saliva supernatant with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.
Label biotin
Label protocol Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
 
Hybridization protocol Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.
Scan protocol Array scanning was performed according to the manufacturer's instruction (Affymetrix)
Description Library files included in primary analysis:
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.clf
HuEx-1_0-st-v2.r2.antigenomic.bgp
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
Data processing Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.
 
Submission date May 21, 2007
Last update date Sep 18, 2008
Contact name David T.W. Wong
E-mail(s) dtww@ucla.edu, mikehu@ucla.edu
Organization name University of California, Los Angeles
Department Dental Research Institute
Street address 10833 Le Conte Ave, CHS 73-017
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL5175
Series (1)
GSE7760 Exon Level Expression Profiling: a Novel Unbiased Transcriptome Analysis for Body Fluids

Data table header descriptions
ID_REF
VALUE RMA expression value derived from Expression Console software; core-exon analysis

Data table
ID_REF VALUE
3948543 2.45077
3063807 3.8626
3096575 2.73845
2949118 5.69173
3227645 4.81688
4014076 1.26737
2637819 1.08144
3850234 3.80447
3719161 3.28316
2916345 1.0247
2342904 3.048
3817464 4.00172
2408437 3.59005
3932148 1.35977
3375091 4.06527
3653619 2.71115
2818035 1.92715
3063795 2.03788
2359282 5.09678
2981874 6.78148

Total number of rows: 22011

Table truncated, full table size 343 Kbytes.




Supplementary file Size Download File type/resource
GSM190747.cel.gz 18.3 Mb (ftp)(http) CEL
GSM190747.chp.gz 176.5 Kb (ftp)(http) CHP
Processed data provided as supplementary file
Processed data included within Sample table

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