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Sample GSM341669 Query DataSets for GSM341669
Status Public on Nov 19, 2008
Title SA01 P83 vs. VUB01 P150
Sample type genomic
 
Channel 1
Source name SA01 P83
Organism Homo sapiens
Characteristics human embryonic stem cells
Biomaterial provider Cellartis AB, Göteborg, Sweden
Growth protocol Human embryonic stem cells grown on STO feeders. Manual dissection was systematically used to passage the cells
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from hESC using the Wizard® Genomic DNA Purification Kit (Promega, Charbonnieres, France).
Label CY5
Label protocol A genomic DNA labeling kit (Enzo, Farmingdale, NY) was used to label the sample DNA with Cy5. The labeled products were purified with QiaQuick polymerase chain reaction (PCR) purification kits (Qiagen, Valencia, CA).
 
Channel 2
Source name VUB01 P150
Organism Homo sapiens
Characteristics human embryonic stem cells
Biomaterial provider Research Centre for Reproduction and Genetics, University Hospital and Medical School of the Vrije Universiteit Brussel, Brussels, Belgium.
Growth protocol Human embryonic stem cells derived as described by Mateizel, I. et al. Hum. Reprod. 21, 503-511 (2006) and grown on STO feeders. Manual dissection was systematically used to passage the cells
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from hESC using the Wizard® Genomic DNA Purification Kit (Promega, Charbonnieres, France).
Label CY3
Label protocol A genomic DNA labeling kit (Enzo, Farmingdale, NY) was used to label the sample DNA with Cy3. The labeled products were purified with QiaQuick polymerase chain reaction (PCR) purification kits (Qiagen, Valencia, CA).
 
 
Hybridization protocol After addition of tRNA (48 mg) plus a quantity of human Cot DNA (Invitrogen, Carlsbad, CA) equal to 50 times the mass of the labeled DNAs, the resulting products were concentrated by vacuum centrifugation, resuspended in 43 mL of hybridization solution (Ambion, Austin, TX) and deposited on the array under a coverslip. Hybridization in a sealed chamber (Corning Life Sciences, Acton, MA) was for 66 hours at 55_C, a post hybridization treatement was done.
Scan protocol Slides were scanned (Agilent Technologies, Santa Clara, CA), data were extracted with GenePix 6 (Axon InstrumentseMolecular Devices, Sunnyvale, CA),
Description DATA exportation with Genocensus software
Data processing All data is lowess normalized, ratio value is CY5/CY3. Copy number analysis was performed with GenoCensus (IntegraGen), which includes block Loess normalization
 
Submission date Nov 12, 2008
Last update date Nov 18, 2008
Contact name Anselme Louis Perrier
E-mail(s) aperrier@istem.genethon.fr
Phone +33 1 69 90 85 23
Fax +33 1 69 90 85 21
URL http://www.istem.eu/
Organization name INSERM/UEVE UMR 861,
Department I-Stem, AFM
Street address 5 rue desbrueres
City Evry cedex
ZIP/Postal code 91000
Country France
 
Platform ID GPL7630
Series (1)
GSE13565 Human ES cells reveal recurrent genomic instability at 20q11.21

Data table header descriptions
ID_REF
Ratio lowess normalized Cy5/Cy3
VALUE lowess normalized log Cy5/Cy3
Valide
Filter

Data table
ID_REF Ratio VALUE Valide Filter
ADELA-4G09 (ADELA-4G09) 1.0069025 0.009923929 true false
ADELA-4G08 (RP11-23D24) 1.041853 0.059151668 true false
ADELA-4G07 (ADELA-4G07) 1.0543592 0.07636645 true false
ADELA-4G06 (RP11-77I5) 1.0645249 0.09020968 true false
ADELA-4G05 (RP11-472A3) 0.99237216 -0.01104684 true false
BPADA-11D09 (RP11-273J1) 1.0339178 0.04812147 true false
ADELA-4G04 (RP11-34G16) 0.98189545 -0.026358683 true false
BPADA-11D08 (RP11-258C19) 0.9582191 -0.061572507 true false
ADELA-4G03 (RP11-458N5) 0.9573144 -0.06293533 true false
BPADA-4A09 (BPADA-4A09) 0.9961613 -0.005548756 false false
BPADA-11D07 (RP11-242D1) 1.0117799 0.01689549 true false
ADELA-4G02 (RP11-25F14) 1.0561078 0.07875705 true false
BPADA-4A08 (BPADA-4A08) 1.0911088 0.12579496 false false
BPADA-11D06 (BPADA-11D06) 0.97354925 -0.038674135 true false
ADELA-4G01 (RP11-513B7) 1.0682741 0.09528192 true false
BPADA-4A07 (BPADA-4A07) 0.9600095 -0.05887939 true false
BPADA-11D05 (RP11-211I3) 0.9546631 -0.0669364 true false
BPADA-4A06 (RP11-29N19) 1.025746 0.036673512 true false
BPADA-11D04 (RP11-196B15) 1.0038234 0.0055054813 true false
BPADA-4A05 (BPADA-4A05) 0.96827704 -0.046508215 true false

Total number of rows: 5878

Table truncated, full table size 331 Kbytes.




Supplementary file Size Download File type/resource
GSM341669.gpr.gz 2.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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