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Sample GSM242751 Query DataSets for GSM242751
Status Public on Sep 16, 2008
Title Spleen_gland_subject1_dye-swap
Sample type genomic
 
Channel 1
Source name Genomic DNA isolated from spleen of subject 1 labeled with Cy5-dCTP.
Organism Homo sapiens
Characteristics Gender: male
Age: 42
Tissue: spleen
Cause of death: acute cardiovascular failure
Extracted molecule genomic DNA
Extraction protocol genomic DNA isolation with phenol extraction according to standard protocol (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning; a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989)
Label Cy5
Label protocol Labeling was done using 2 mcg DNA, according to the BioPrime® Array CGH Genomic Labeling System protocol supplied by the manufacturer (Invitrogen, Carlsbad, CA). We used CY3 dCTP and CY5 dCTP respectively (PA53021 and PA55021, GE Healthcare, Piscataway, NJ). The labeled DNA probes were mixed together and combined with 200 µg human Cot-1 DNA (Invitrogen, Carlsbad, CA) and dried using a vacufuge concentrator (Eppendorf, Westbury, NY).
 
Channel 2
Source name Genomic DNA isolated from cerebellum of subject 1 labeled with Cy3-dCTP.
Organism Homo sapiens
Characteristics Gender: male
Age: 42
Tissue: brain-cerebellum
Cause of death: acute cardiovascular failure
Extracted molecule genomic DNA
Extraction protocol genomic DNA isolation with phenol extraction according to standard protocol (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning; a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989)
Label Cy3
Label protocol Labeling was done using 2 mcg DNA, according to the BioPrime® Array CGH Genomic Labeling System protocol supplied by the manufacturer (Invitrogen, Carlsbad, CA). We used CY3 dCTP and CY5 dCTP respectively (PA53021 and PA55021, GE Healthcare, Piscataway, NJ). The labeled DNA probes were mixed together and combined with 200 µg human Cot-1 DNA (Invitrogen, Carlsbad, CA) and dried using a vacufuge concentrator (Eppendorf, Westbury, NY).
 
 
Hybridization protocol The 32K slides were prehybridized in 5x SCC, 0.1% SDS at 45 ºC for at least one hour, washed with ddH20 and dried using compressed dust-free air. The dried pellets from the labeling steps were re-suspended in 50 µl of hybridization solution (50% Formamide, 4% SDS, 10 %, Dextran Sulfate, M.W. 500 000, 2 X SSC) and denatured for 5 min at 95°C, followed by incubation at 45°C for 2 h to block repetitive sequences. Subsequently, the probe mixture was applied to the slide surface, covered with a lifterslip (22x60mm, Erie Scientific, Portsmouth, NH) and hybridized at 45 °C for 20 hours in a slide chamber (Corning Inc. Life Sciences, Big Flats, NY). After hybridization the lifterslip was rinsed off using 1xPBS. Washing was performed in 25 % formamide, 2 X SSC, 0.1% SDS, at 45ºC, for 15 min, followed by 10 min in 1 X PBS at room temperature, and brief rinse in 0.2 X SSC. The array was immersed in deionized H2O and immediately dried using pressurized dust-free air.
Scan protocol Image acquisition was performed using the GenePix 4000B scanner (Axon Instruments Inc, Union City, CA), and image analysis was carried out using the GenePixPro v6 software (Axon Instruments).
Description none
Data processing We uploaded the GPR files from GenePix pro into a pearl script called colloactor. This script links the information about clones to the array position. It also uploads the raw data to the BASE platform. These raw data files are attached as tables. Filtering and normalization was done using the LCB Data-WareHouse (dw.lcb.uu.se). The filters applied on the raw data removed spots containing more than 5% oversaturated pixels, spots with low Signal-to-Noise Ratio (SNR<3) and spots automatically and manually flagged as bad, absent or not found in GenePixPro program. Normalization was done using a print-tip loess method.
 
Submission date Nov 13, 2007
Last update date Aug 14, 2011
Contact name Jan Dumanski
E-mail(s) jdumanski@genetics.uab.edu
Phone 205 996 4045
Fax 205 996 4056
URL http://www.genetics.uab.edu/Faculty/
Organization name University of Alabama at Birmingham
Department Department of Genetics
Lab Howell and Elizabeth Heflin Center for Human Genetics
Street address 1530 3rd. Ave. S., Kaul 420
City Birmingham
State/province AL
ZIP/Postal code 35294
Country USA
 
Platform ID GPL6088
Series (1)
GSE9598 Somatic mosaicism for copy number variation in differentiated human tissues

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy3/Cy5 - regular hybridization, Cy5/Cy3 - dye-swap hybridization)

Data table
ID_REF VALUE
1
2 -0.041
3 0.263
4 0.211
5 -0.161
6 0.022
7 0
8 0.252
9 0.126
10 -0.024
11 0.08
12 -0.055
13 -0.039
14
15
16 0.009
17 0.181
18 -0.07
19 -0.025
20 -0.06

Total number of rows: 32918

Table truncated, full table size 351 Kbytes.




Supplementary file Size Download File type/resource
GSM242751.tab.gz 3.6 Mb (ftp)(http) TAB
Processed data included within Sample table

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