NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM401434 Query DataSets for GSM401434
Status Public on May 20, 2009
Title MPNST-10_cy3
Sample type genomic
 
Channel 1
Source name MPNST
Organism Homo sapiens
Characteristics tissue: malignant peripheral nerve sheath tumours
disease state: malignant tumor
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 Two micrograms DNA was labelled using CY3 dCTP and CY5 dCTP (PA53021 and PA55021 respectively, GE Healthcare, Piscataway, NJ) according to the BioPrime® Array CGH Genomic Labeling System protocol (Invitrogen, Carlsbad, CA).The labeled DNA probes were mixed together and combined with 200 µg human Cot-1 DNA (Invitrogen, Carlsbad, CA) and dried using a vaccum centrifuge.
 
Channel 2
Source name Peripheral blood derived DNA
Organism Homo sapiens
Characteristics tissue: peripheral blood
disease state: normal
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 Two micrograms DNA was labelled using CY3 dCTP and CY5 dCTP (PA53021 and PA55021 respectively, GE Healthcare, Piscataway, NJ) according to the BioPrime® Array CGH Genomic Labeling System protocol (Invitrogen, Carlsbad, CA).The labeled DNA probes were mixed together and combined with 200 µg human Cot-1 DNA (Invitrogen, Carlsbad, CA) and dried using a vaccum centrifuge.
 
 
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 n/a
Data processing We uploaded the GPR files from GenePix pro into a perl 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 May 11, 2009
Last update date May 19, 2009
Contact name Kiran Kumar Mantripragada
Organization name Cardiff University
Department Medical Genetics
Street address Heath Park Campus
City Cardiff
ZIP/Postal code CF14 4XN
Country United Kingdom
 
Platform ID GPL6088
Series (1)
GSE16041 Array-CGH of malignant peripheral nerve sheath tumors (MPNST)

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio test/reference

Data table
ID_REF VALUE
1 -0.01
2 -0.31
3 0.18
4
5 0.16
6 -0.27
8 -0.16
7 -0.21
9 0.1
10 -0.12
11 -0.04
12 0.04
13 0.13
14 -0.17
15 0.12
16 -0.27
17 0.1
18 0.05
19 0.01
20 0.1

Total number of rows: 32316

Table truncated, full table size 332 Kbytes.




Supplementary file Size Download File type/resource
GSM401434.gpr.gz 3.5 Mb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.