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Sample GSM341660 Query DataSets for GSM341660
Status Public on Nov 19, 2008
Title H1 P41 vs. Control
Sample type genomic
 
Channel 1
Source name H1 P41
Organism Homo sapiens
Characteristics human embryonic stem cells
Biomaterial provider Wisconsin Alumni Research Foundation, Madison, WI, USA
Growth protocol Human embryonic stem cells derived 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 CY3
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 control male 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 CY5
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 GPL7629
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
DBACA-3B11 (RP11-411H5) 0.9538523 -0.06816221 true false
DBACA-14D03 (RP11-192M1) 1.1557678 0.20885158 true false
IGGAP-23E10 (RP11-586I21) 1.0375097 0.053124797 true false
ADELA-9G05 (RP11-685N10) 0.960679 -0.05787365 true false
DBACA-15C11 (RP11-335H4) 1.0226614 0.03232862 true false
BPADA-8E03 (RP11-14N24) 0.97046196 -0.043256424 true false
DBACA-24C10 (DBACA-24C10) 0.96851623 -0.04615187 true false
DBACA-5F10 (DBACA-5F10) 0.9149313 -0.12826468 true false
DBACA-15B05 (RP11-526P6) 0.95058626 -0.07311055 true false
IGGAP-24C11 (RP11-807F23) 1.0440686 0.062216472 true false
CURIE-14G10 (RP11-122A4) 0.95334715 -0.06892645 true false
CURIE-16D02 (CURIE-16D02) 0.91795355 -0.12350694 true false
IGGAP-22F05 (IGGAP-22F05) 0.99933356 -9.617895E-4 true false
CURIE-14C08 (RP11-100C2) 0.9415863 -0.08683474 true false
DBACA-19C04 (DBACA-19C04) 0.9541857 -0.06765799 false false
IGGAP-24D04 (RP11-683L23) 1.0410132 0.05798842 true false
DBACA-18A03 (CTB-40M15) 0.9526841 -0.06993018 true false
IGGAP-22E07 (RP11-242B20) 1.1070901 0.14677265 true false
APADA-2B07 (RP11-379B8) 0.88594365 -0.17471315 true false
BPADA-6B09 (BPADA-6B09) 0.9459858 -0.080109574 true false

Total number of rows: 5508

Table truncated, full table size 310 Kbytes.




Supplementary file Size Download File type/resource
GSM341660.gpr.gz 2.6 Mb (ftp)(http) GPR
Processed data included within Sample table

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