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Sample GSM341553 Query DataSets for GSM341553
Status Public on Nov 19, 2008
Title SA01 P49
Sample type genomic
 
Source name SA01 P49
Organism Homo sapiens
Characteristics human embryonic stem cells
Biomaterial provider Cellartis AB, Göteborg, Sweden
Growth protocol Human embryonic stem cells derived by Cellartis AB and cultured on STO feeder cells in DMEM-F12 medium supplemented with 4ng/ml FGF2
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from hESC using the Wizard® Genomic DNA Purification Kit (Promega, Charbonnieres, France).
Label CY3, CY5
Label protocol For the single-base extension (SBE) (Infinium II) assay, primers were extended with a polymerase and labeled nucleotide mix (TEM), and stained with repeated application of LTM (staining reagent) and ASM (anti-staining reagent). After staining was complete, the slides were washed with low salt wash buffer (PB1), immediately coated with XC4, and then imaged on the Illumina BeadArray Reader.
 
Hybridization protocol The whole-genome amplification process requires 250–750 ng of input gDNA and creates a sufficient quantity of DNA (1000× amplification) to be used on a single BeadChip in the Infinium assay (Illumina MP1 and AMM). After amplification, the product is fragmented using a proprietary reagent (FRG), precipitated with 2-propanol (plus precipitating reagent; PA1), and resus-pended in formamide-containing hybridization buffer (RA1). The DNA samples are denatured at 95°C for 20 min, loaded into the Tecan Flow Through Chambers (Tecan Part No. 760,810), and placed in a humidified container for a minimum of 16 h at 48°C allowing SNP loci to hybridize to the 50mer capture probes (Steemers and Gunderson 2005).
Scan protocol The Illumina BeadArray Reader is a two-color (543 nm/643 nm) confocal fluorescent scanner with 0.84-μm pixel resolution. The scanner excites the fluorophors generated during signal amplification/staining of the allele-specific (one color) or single-base (two colors) extension products on the BeadChips. The image intensities are extracted using Illumina's BeadScan software.
Description HumanHap300 (317,000 tag SNPs) Genotyping BeadChips from Illumina apply to the 550K array (HumanHap550)
Data processing The data for each BeadChip is self-normalized using information contained within the array. This normalization algorithm removes outliers, adjusts for channel-dependent background and global intensity differences, and also scales the data.
 
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 GPL6980
Series (1)
GSE13565 Human ES cells reveal recurrent genomic instability at 20q11.21

Data table header descriptions
ID_REF
VALUE Genotype: AA,AB,BB,or NC (no call)
Confidence_Score Beadstudio confidence score
Theta Beadstudio genotype metric
R Beadstudio intensity metric
B_Allele_Freq Beadstudio estimate of B allele frequency
Log_R_ratio Beadstudio metric for signal intensity

Data table
ID_REF VALUE Confidence_Score Theta R B_Allele_Freq Log_R_ratio
rs10000010-126_B_F_IFB1153208421:0 BB 0.9368909 0.9832261 0.8866378 0.9907788 -0.1222613
rs10000023-126_B_F_IFB1153358872:0 BB 0.8234195 0.9847338 1.716692 1 -0.01580486
rs10000030-120_B_R_IFB1137703207:0 NC 0.1167757 0.6909122 0.5849801 0.4403135 -0.04677175
rs1000007-123_T_F_IFB1152225452:0 AB 0.8747823 0.5975847 1.050611 0.4543363 0.02785094
rs10000092-123_T_R_IFB1153358875:0 AA 0.9264655 0.009770006 0.809898 0.002422354 0.1027358
rs10000121-126_B_R_IFB1136471760:0 BB 0.891854 0.985224 0.4874392 1 -0.3630315
rs1000014-126_B_R_IFB1136184019:0 BB 0.7254323 0.948649 1.580925 0.982752 0.1413279
rs10000141-126_T_F_IFB1137734411:0 BB 0.8891098 0.9959394 0.7805151 1 -0.2389937
rs1000016-126_B_R_IFB1156563530:0 AA 0.875866 0.009045174 1.940275 0.007525917 0.1261717
rs10000169-119_T_R_IFB1135612081:0 AA 0.8703538 0.01300503 1.171537 0.004849787 0.2229694
rs1000022-126_B_F_IFB1135126284:0 AB 0.8797732 0.5836014 1.015741 0.4594404 0.2258663
rs10000272-126_T_R_IFB1136539894:0 AA 0.8434824 0.009349082 1.645314 0.008218159 -0.199565
rs10000282-121_T_R_IFB1136743500:0 BB 0.8183947 0.9836101 1.268481 0.9978786 0.07785132
rs10000300-126_T_R_IFB1152704058:0 AB 0.8601294 0.5491947 0.7968401 0.4596424 0.2044196
rs1000031-123_B_F_IFB1135583872:0 AB 0.8717313 0.4887917 2.269524 0.523502 -0.007997355
rs1000032-126_B_R_IFB1136145093:0 BB 0.384529 0.987204 1.505097 1 0.4085742
rs10000388-126_B_F_IFB1135932472:0 AA 0.9530174 0.02031875 1.173827 0.01299723 -0.2104887
rs1000040-126_T_F_IFB1152704061:0 AA 0.8484263 0.01369831 1.145663 0.0001711198 0.4651628
rs1000041-126_T_F_IFB1153889147:0 BB 0.8351063 0.9811666 1.453316 0.9994189 0.051941
rs10000432-126_T_R_IFB1135756304:0 AB 0.8544981 0.6727884 0.5857296 0.4765959 -0.2486354

Total number of rows: 318237

Table truncated, full table size 26405 Kbytes.




Supplementary file Size Download File type/resource
GSM341553.txt.gz 20.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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