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Sample GSM341589 Query DataSets for GSM341589
Status Public on Nov 19, 2008
Title VUB05-HD P103 vs. Control
Sample type genomic
 
Channel 1
Source name VUB05-HD P103
Organism Homo sapiens
Characteristics male 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 grown on STO feeders. Manual dissection was systematically used to passage the cells rather than enzymatic methods.
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 Control
Organism Homo sapiens
Characteristics Female human genomic DNA
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 GPL7626
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
CURIE-16G11 (CURIE-16G11) 1.0851772 0.11793062 true false
DBACA-3B11 (RP11-411H5) 1.0063516 0.0091344295 true false
DBACA-14D03 (RP11-192M1) 0.956634 -0.06396105 true false
IGGAP-23E10 (RP11-586I21) 1.0000029 4.1275775E-6 true false
ADELA-9G05 (RP11-685N10) 1.0150931 0.021612035 true false
DBACA-15C11 (RP11-335H4) 0.8108154 -0.3025546 true false
BPADA-8E03 (RP11-14N24) 1.021934 0.031302072 true false
DBACA-15B05 (RP11-526P6) 1.0027514 0.003963909 true false
IGGAP-24C11 (RP11-807F23) 3.7367554 1.9017861 true false
CURIE-14G10 (RP11-122A4) 1.0553819 0.07776514 true false
CURIE-14C08 (RP11-100C2) 1.0789927 0.10968514 true false
IGGAP-24D04 (RP11-683L23) 1.0254203 0.036215376 true false
DBACA-18A03 (CTB-40M15) 1.0211314 0.03016852 true false
IGGAP-22E07 (RP11-242B20) 0.9148257 -0.12843123 true false
APADA-2B07 (RP11-379B8) 1.0528857 0.07434876 true false
BPADA-9F10 (BPADA-9F10) 1.021332 0.03045195 true false
DBACA-21F02 (CTA-190C6) 0.9284358 -0.10712594 true false
ADELA-4B07 (RP11-41F5) 0.9570245 -0.06337222 true false
ADELA-4A11 (RP11-481K16) 0.0 #NOM? true true
ADELA-10B08 (RP11-139K6) 0.96894026 -0.04552038 true false

Total number of rows: 5152

Table truncated, full table size 291 Kbytes.




Supplementary file Size Download File type/resource
GSM341589.gpr.gz 2.6 Mb (ftp)(http) GPR
Processed data included within Sample table

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