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Sample GSM74521 Query DataSets for GSM74521
Status Public on Dec 19, 2005
Title GM01750_b42_s51
Sample type genomic
 
Channel 1
Source name GM01750
Organism Homo sapiens
Characteristics fibroblast cell line
Gender: male
ISCN: 47,XY,+der(14)t(9;14)(14pter>14q21:: 9p24>9pter)mat
as described: http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM01750
Biomaterial provider Coriell Institute for medical research (http://locus.umdnj.edu/nigms)
Coriell
Treatment protocol none
Growth protocol as described: http://locus.umdnj.edu/nigms/nigms_cgi/display.cgi?GM01750
Extracted molecule genomic DNA
Extraction protocol DNA isolation protocol available via www.vumc.nl/microarrays
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192
Label Cy3
Label protocol DNA labeling protocol available via www.vumc.nl/microarrays
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192
 
Channel 2
Source name female reference DNA
Organism Homo sapiens
Characteristics Pooled DNA from the blood of 10 normal female individuals
Biomaterial provider VUMC, Amsterdam
Coriell
Treatment protocol none
Growth protocol n.a.
Extracted molecule genomic DNA
Extraction protocol DNAzol (Invitrogen) according to manufacturer's protocol
Label Cy5
Label protocol DNA labeling protocol available via www.vumc.nl/microarrays
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192
 
 
Hybridization protocol Hybridization protocol available via www.vumc.nl/microarrays
Also described in Van den IJssel et al, Nucleic Acids Res. 2005 Dec 16;33(22):e192
Scan protocol Microarray Scanner G2505B (Agilent Technologies), default settings
Description For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).
Data processing Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA) and The Sanger Institute (Hinxton, Cambridge, UK), respectively, via www.ensembl.org. A unique chromosomal position was identified for 26845 of 28830 oligonucleotides in the human library. Oligonucleotides were excluded when they mapped to more than one position in the genome or showed one or more mismatches with regard to the current build. Log2ratio’s of spots that were not excluded after quality flagging and mapping were normalized to their mode value. Weighted moving average values were then calculated using a triangular function and a window of 250 kb as described (Barrett,M.T. et al. (2004) Proc.Natl.Acad.Sci.U.S.A, 101, 17765-17770.).
 
Submission date Sep 16, 2005
Last update date Dec 22, 2005
Contact name Daoud Sie
E-mail(s) d.sie@vumc.nl
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
 
Platform ID GPL2819
Series (1)
GSE3264 Oligonucleotide-based arrayCGH

Data table header descriptions
ID_REF
AMPCH1 Total signal in channel 1 (Cy3)
AMPCH2 Total signal in channel 2 (Cy5)
LOG2RATIO CH1/CH2 Log, base 2, of the ratio of total signal in channel 1 divided by total signal in channel 2
CONFIDENCE The Confidence Estimate in the calculated ratio, between 0 and 1, calculated by BlueFuse
QUALITY A flag to highlight spots that suffer from poor printing and other experimental artefacts (1 acceptable; 0 not acceptable), estimated by BlueFuse
VALUE Mode normalized value of the log2ratio, replicates are fused by BlueFuse, features with confidenc < 0.1 or quality 0 are excluded
MOVING_AVERAGE weighted moving average with a window of 250 kb

Data table
ID_REF AMPCH1 AMPCH2 LOG2RATIO CH1/CH2 CONFIDENCE QUALITY VALUE MOVING_AVERAGE
1 577.547 1130.583 -0.969 0.86 0
2 446.404 772.855 -0.792 0.97 1 0.013 0.207776143
3 493.031 909.154 -0.883 0.86 1 -0.078 -0.04254289
4 1326.203 2134.971 -0.687 0.69 1 0.118 0.144031187
5 1428.036 2296.75 -0.686 0.96 1 0.119 0.168099904
6 1245.376 2041.13 -0.713 0.7 1 0.092 0.011983793
7 298.576 505.343 -0.759 0.83 1 0.046 -0.040440141
8 805.274 1392.989 -0.791 0.87 1 0.014 -0.118008423
9 301.959 718.14 -1.25 0.86 1 -0.445 -0.031395763
10 521.415 1152.406 -1.144 0.98 1 -0.339 0.002828854
11 402.984 879.246 -1.126 0.86 1 -0.321 -0.1599527
12 769.681 1431.615 -0.895 0.88 1 -0.09 -0.024634201
13 336.618 604.657 -0.845 0.87 1 -0.04 -0.022798749
14 614.093 1315.274 -1.099 0.98 1 -0.294 -0.005449615
15 523.343 1011.278 -0.95 0.98 1 -0.145 -0.058751061
16 512.536 1330.59 -1.376 0.86 1 -0.571 -0.104423373
17 611.942 1200.735 -0.972 0.97 1 -0.167 -0.086413938
18 279.053 525.649 -0.914 0.69 1 -0.109 -0.14172046
19 398.572 754.023 -0.92 0.84 0
20 853.589 1728.033 -1.018 0.95 0

Total number of rows: 30000

Table truncated, full table size 1512 Kbytes.




Supplementary data files not provided

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