|
| Status |
Public on Aug 01, 2011 |
| Title |
Peripheral blood healthy control C004_Xba |
| Sample type |
genomic |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Peripheral blood healthy control
subject id: C004
gender: female
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was obtained from cell lines or peripheral blood with PureLink genomic DNA kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
|
| Label |
biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to Mapping50K_Xba240
|
| Data processing |
CEL files and CHP files (generated by Affymetrix GeneChip Command Console using the BRLMM algorithm) were processed by Affymetrix Genotyping Console 4.0. For this analysis, the protocol of un-paired samples was followed. Briefly, the parameters were set as follows: quantile normalization was performed at the perfect match (PM) probe level, followed by summarization of the signal intensity for each allele of each SNP. Genomic smoothing was set to 0.5 Mb and a five state Hidden Markov Model (HMM) was applied for smoothing and segmenting CN data. The different states were defined as follows: 0=homozygous deletion; 1=heterozygous deletion; 2=normal diploid; 3=single copy gain and 4=amplification. Each SNP was fitted to one of the possible CN states with a transition decay of 10 Mb and a threshold for SNP outlier of 1000 bp.
CHP files of 4 cell lines and 38 healty controls.
|
| |
|
| Submission date |
May 12, 2011 |
| Last update date |
Aug 01, 2011 |
| Contact name |
Jaime Berumen |
| E-mail(s) |
[email protected]
|
| Phone |
+52(55)27892000
|
| Organization name |
Universidad Nacional Autonoma de Mexico
|
| Department |
Departamento de Medicina Experimental
|
| Lab |
Unidad de Medicina Genómica
|
| Street address |
Dr. Balmis #148 Col. Doctores
|
| City |
Mexico City |
| ZIP/Postal code |
06726 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL2005 |
| Series (2) |
| GSE29244 |
Amplified genes are not necessarily over expressed, they can be unchanged or down regulated in cervical cancer cell lines [SNP array data] |
| GSE29245 |
Amplified genes are not necessarily over expressed, they can be unchanged or down regulated in cervical cancer cell lines |
|
