|
| Status |
Public on Aug 01, 2020 |
| Title |
ASD 61 |
| Sample type |
genomic |
| |
|
| Source name |
genomic DNA from peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Autism spectrum disorder (ASD)
race: Japanese
gender: female
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from peripheral blood were extracted using QIAamp DNA Blood Mini kit (QIAGEN, Hilden, Germany) in accordance with manufacturer's instructions. 500 ng of genomic DNA was carried out to digestion by Sty and Nsp.
|
| Label |
biotin
|
| Label protocol |
Fragmented DNA were subjected to 3' terminal labeling with TdT enzyme.
|
| |
|
| Hybridization protocol |
Hybridization were carried out using the SNP 6 Core Reagent Kit and a GeneAmp® PCR System 9700 in accordance with manufacture's instructions. Samples were loaded onto the arrays to rotate in the hybridization oven (GeneChip® Hybridization Oven 645) for 18 hours at 50℃ and 60 rpm. After hybridization, the arrays were washed and stained using GenomeWideSNP6_450 protocol for the Fluidics Station 450.
|
| Scan protocol |
GeneChips® were scanned using the GeneChip® Scanner 3000 7G controlled by Affymetrix GeneChip® Command Console® software.
|
| Description |
Genome-Wide Human SNP Array 6.0
|
| Data processing |
Generated CEL files were conducted to normalize signal intensities using Genotyping Console. Copy number states were derived from a Hidden Markov Model based algorithm implemented Birdseed v2.
Copy number state: 0, 1, 2, 3, 4
|
| |
|
| Submission date |
Feb 07, 2020 |
| Last update date |
Aug 02, 2020 |
| Contact name |
Shuji Shimoyama |
| E-mail(s) |
shuji-s@hirosaki-u.ac.jp
|
| Phone |
+81-172-39-5138
|
| Organization name |
Hirosaki University Graduate School of Medicine
|
| Department |
Department of Neurophysiology
|
| Street address |
5 Zaifu-cho
|
| City |
Hirosaki |
| State/province |
Aomori |
| ZIP/Postal code |
036-8562 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE144918 |
Copy number variation analysis in Japanese children with Autsim Spectrum Disorder by Affymetrix Genome-Wide Human SNP Array 6.0. |
|
