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Sample GSM1941819 Query DataSets for GSM1941819
Status Public on May 01, 2016
Title Fibroblast cell line F3, cell 11, sister cell 2
Sample type genomic
 
Channel 1
Source name Reference DNA
Organism Homo sapiens
Characteristics sample type: reference
gender: Male
Treatment protocol Single fibroblasts were plated separately and the two cells that derived following a cell division were isolated individually.
Growth protocol Primary fibroblasts were grown in 75-cm2 plastic flasks (BD Falcon, USA) under standard culture conditions in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium complemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA).
Extracted molecule genomic DNA
Extraction protocol The genome of collected single cells was amplified using the Sureplex amplification system (BlueGnome/Illumina, USA).
Label Cy3
Label protocol The fluorescent labeling system (BlueGnome/Illumina) was used for sample labeling. Samples and Reference DNAs were labeled using Cy5 or Cy3 for 2-4h at 37░C. Samples were combined with the respective references prior to hybridization.
 
Channel 2
Source name Primary single fibroblast, F3
Organism Homo sapiens
Characteristics cell type: primary single fibroblast
gender: Female
Treatment protocol Single fibroblasts were plated separately and the two cells that derived following a cell division were isolated individually.
Growth protocol Primary fibroblasts were grown in 75-cm2 plastic flasks (BD Falcon, USA) under standard culture conditions in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium complemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA).
Extracted molecule genomic DNA
Extraction protocol The genome of collected single cells was amplified using the Sureplex amplification system (BlueGnome/Illumina, USA).
Label Cy5
Label protocol The fluorescent labeling system (BlueGnome/Illumina) was used for sample labeling. Samples and Reference DNAs were labeled using Cy5 or Cy3 for 2-4h at 37░C. Samples were combined with the respective references prior to hybridization.
 
 
Hybridization protocol 200 ng of sample DNA and equal amount of commercially available reference DNA of the were labeled for 2 h by random primer labeling (BlueGnome/Illumina, USA) using Cy5- and Cy3-dCTPs, respectively.
Scan protocol DNA-microarray scanner (Agilent Technologies, UK).
Description Sureplex whole genome amplified single-cell DNA
131
Data processing Separation of the duplex raw images by ImageViewer and the analysis of the data by BlueFuse v3.0 software (BlueGnome/Illumina, USA).
 
Submission date Nov 16, 2015
Last update date May 01, 2016
Contact name Eftychia Dimitriadou
E-mail(s) eftychia.dimitriadou@med.kuleuven.be
Organization name KU Leuven
Lab Cytogenetics and Genome Research
Street address Herestraat 49, ON1, bus 602
City Leuven
ZIP/Postal code 3000
Country Belgium
 
Platform ID GPL21146
Series (2)
GSE75065 Segmental chromosomal imbalances arise at high frequency in human fibroblasts (BAC array)
GSE75116 Segmental chromosomal imbalances arise at high frequency in human fibroblasts

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
1 -0.105
2 -0.124
3 -0.118
4 -0.082
5 -0.198
6 -0.146
7 -0.011
8 -0.166
9 -0.000
10 -0.129
11 -0.127
12 -0.140
13 -0.073
14 -0.095
15 -0.129
16 -0.118
17 -0.084
18 -0.194
19 0.072
20 -0.017

Total number of rows: 10400

Table truncated, full table size 120 Kbytes.




Supplementary file Size Download File type/resource
GSM1941819_F3_11b.gpr.gz 750.8 Kb (ftp)(http) GPR
Processed data included within Sample table

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