|
| Status |
Public on Jul 07, 2022 |
| Title |
amniotic fluid S24-750knsp |
| Sample type |
genomic |
| |
|
| Source name |
amniotic fluid S24
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: amniotic fluid
ultrasound abnormality classification: Non-isolated GITO
obstruction level classification: Duodenal atresia/stenosis
|
| Treatment protocol |
None
|
| Growth protocol |
Cell were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from uncultured amniotic fluid, fetal cord blood using a QIAGEN kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
|
| 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 750K_Nsp
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software (ChAS 4.0). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
primary data description:
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
|
| |
|
| Submission date |
May 16, 2022 |
| Last update date |
Jul 07, 2022 |
| Contact name |
Xiaoqing Wu |
| E-mail(s) |
wuxiaoqing013@126.com
|
| Phone |
+8618650789891
|
| Organization name |
Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University
|
| Street address |
18 daoshan road, Gulou district
|
| City |
Fuzhou |
| ZIP/Postal code |
350001 |
| Country |
China |
| |
|
| Platform ID |
GPL18637 |
| Series (1) |
| GSE203126 |
Chromosomal abnormalities and pregnancy outcomes for fetuses with gastrointestinal tract obstructions |
|
