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Sample GSM187390 Query DataSets for GSM187390
Status Public on Aug 29, 2007
Title Somatic_cell_line_19822_ReplicateB
Sample type RNA
 
Source name Rhesus monkey adult skin fibroblast somatic cell line 19822 biological replicate B
Organism Macaca mulatta
Characteristics A differentiated rhesus monkey adult skin fibroblast somatic cell line derived from a nine year old adult male animal (Oregon National Primate Research Center ID:19822). Biological replicate B.
Biomaterial provider James A. Byrne, PhD
Treatment protocol Cells were manually removed from culture with a cell scraper without using trypsin.
Growth protocol Somatic cells were grown at 37°C in 5% CO2 atmosphere in Dulbecco’s Modified Eagle’s Medium (DMEM) (Invitrogen) supplemented with 10% foetal bovine serum (FBS).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from complete dishes of 90% confluent somatic cells using the Invitrogen TRIZOL reagent, followed by further purification with the Qiagen RNeasy MinElute Cleanup Kit. The RNA samples were quantified using the NanoDrop ND-1000 UV-Vis spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the quality of the RNA was assessed using Lab-on-a-Chip RNA Pico Chips and the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label Biotin
Label protocol Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)
 
Hybridization protocol Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)
Scan protocol Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). Scanning Hardware – HP GeneArray Scanner
Description Probe level measurements produced by Affymetrix Microarray Suite 5.0. Analysis performed at level of raw signal. (See Affymetrix Microarray Suite 5.0 reference on web site for description).
Data processing MAS 5.0; Data was normalized with Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001). Two .CHP files are provided as supplementary files: one normalized (_GS.CHP) and one not (.CHP).
 
Submission date May 04, 2007
Last update date May 07, 2007
Contact name James Anthony Byrne
E-mail(s) byrnej@ohsu.edu
Phone 5036905335
Organization name ONPRC
Department Reproductive Sciences
Lab Wolf lab
Street address 505 NW 185th Ave
City Beaverton
State/province OR
ZIP/Postal code 97006
Country USA
 
Platform ID GPL3535
Series (1)
GSE7748 Transcriptional profiling of rhesus monkey nuclear transfer embryonic stem cells

Data table header descriptions
ID_REF
VALUE Probe set signal (SG) for somatic donor cell line biological replicate B
ABS_CALL Probe set detection (DT) for somatic donor cell line biological replicate B
DETECTION P-VALUE Probe set detection P-value (DP) for somatic donor cell line biological replicate B

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-3_at 178.8 P 0.000044
AFFX-BioB-5_at 217.7 P 0.000662
AFFX-BioB-M_at 375.8 P 0.000044
AFFX-BioC-3_at 808 P 0.000044
AFFX-BioC-5_at 642.6 P 0.000052
AFFX-BioDn-3_at 3411 P 0.000052
AFFX-BioDn-5_at 1754 P 0.000044
AFFX-CreX-3_at 10471.2 P 0.000044
AFFX-CreX-5_at 8362.7 P 0.000052
AFFX-DapX-3_at 1.3 A 0.976071
AFFX-DapX-5_at 1.7 A 0.686292
AFFX-DapX-M_at 11.4 A 0.58862
AFFX-LysX-3_at 4 A 0.368438
AFFX-LysX-5_at 6 A 0.5
AFFX-LysX-M_at 1.7 A 0.969024
AFFX-Mmu-actin-3_s_at 14466.1 P 0.000244
AFFX-Mmu-actin-5_at 10488 P 0.000244
AFFX-Mmu-actin-M_at 14972.3 P 0.000244
AFFX-Mmu-actin-M_x_at 14024.8 P 0.000244
AFFX-Mmu-ef1a-3_x_at 13863 P 0.000244

Total number of rows: 52865

Table truncated, full table size 1921 Kbytes.




Supplementary file Size Download File type/resource
GSM187390.CEL.gz 4.9 Mb (ftp)(http) CEL
GSM187390.CHP.gz 300.2 Kb (ftp)(http) CHP
GSM187390.RPT.gz 1023 b (ftp)(http) RPT
GSM187390.xml.gz 4.7 Kb (ftp)(http) XML
GSM187390_GS.CHP.gz 299.9 Kb (ftp)(http) CHP
Processed data provided as supplementary file

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