|
| Status |
Public on Mar 25, 2011 |
| Title |
Genomic DNA extracted from THP-1 cells Replicate 1 |
| Sample type |
genomic |
| |
|
| Source name |
Genomic DNA extracted from THP-1 cells Replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: acute monocytic leukemia
cell line: THP-1
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Qiagen DNA Mini 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 |
XY-2010-g1
|
| Data processing |
Genotyping Console Software Processed data: CEL files were generated by GeneChip® Command Console® Software (AGCC). CHP files for SNP genotyping were generated by Affymetrix Genotyping Consle software using the Birdseed algorithm, CNVCHP files for copy number polymorphism analysis were generated by Affymetrix Genotyping Consle software using the Canary algorithm, and CN5.CNCHP files were generated by Affymetrix Genotyping Consle software using the BRLMM-P+ algorithm. Normalization was performed using the HAPMAP270 reference provided in Affymetrix Genotyping Consle software. The array data were also processed using Birdsuite software and PICNIC software.
primary data description - CHP file: Genotype Call Codes (SNP call): AA, AB, BB, NC, and NoCall; Confidence; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B
|
| |
|
| Submission date |
Mar 23, 2011 |
| Last update date |
Mar 25, 2011 |
| Contact name |
Yan Shea (Xie) |
| E-mail(s) |
clintonrlee@gmail.com
|
| Organization name |
Wuhan University Zhongnan Hospital
|
| Street address |
Donghu Road 169#
|
| City |
Whan |
| State/province |
Hubei |
| ZIP/Postal code |
430071 |
| Country |
China |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE28132 |
Affymetrix SNP 6.0 array data for single cell multiple displacement amplification |
|
