|
| Status |
Public on May 25, 2018 |
| Title |
Sample34: Umbilical cord blood - PTSDDep |
| Sample type |
RNA |
| |
|
| Source name |
Umbilical cord blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Umbilical cord blood
maternal diagnosis: PTSDDep
neonate gender: Female
rin: 8.9
microarray batch: Two
|
| Treatment protocol |
Umbilical cord blood was collected by trained staff after offspring delivery but before delivery of the placenta. The cord was clamped and cut, after which the clamp was released and cord blood drained by gravity into a kidney collection dish. Cord blood was collected using a syringe for processing and storage at -80C in PAXgene RNA tubes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from PAXgene RNA tubes as per the manufacturer's instructions. All samples had a Bioanalyzer RNA Integrity Number (RIN) >7.
|
| Label |
biotin
|
| Label protocol |
Complementary DNA was derived from RNA and then hybridized, and raw probe intensities were generated on Illumina HumanHT-12 v4 BeadChip arrays.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
rep1
|
| Data processing |
All statistical analyses were conducted in the statistical package R. All gene expression data were processed, normalized and quality treated. Raw data were background corrected, quantile normalized and log2 ransformed using the neqc function of limma, a robust method for Illumina BeadChips. Non-specific filtering retained probes expressed in at least 50 arrays with a detection P-value <0.05. When multiple microarray probes mapped to the same HGNC symbol, we used a median reduction technique and used the resulting collapsed expression profile for each gene for further analysis. Resulting normalized data were inspected for outlying samples using unsupervised hierarchical clustering of samples and principal component analysis to identify potential outliers outside two standard deviations from these grand averages. Based on these metrics, 19 samples were labeled as outliers and 149 samples passed into the subsequent analyses.
|
| |
|
| Submission date |
May 24, 2018 |
| Last update date |
May 25, 2018 |
| Contact name |
Michael S Breen |
| Organization name |
Ichan School of Medicine at Mount Sinai
|
| Department |
Depts. of Psychiatry, Genetics and Genomic Sciences
|
| Street address |
1468 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE114852 |
Gene expression in cord blood links genetic risk for neurodevelopmental disorders with maternal psychological distress and adverse childhood outcomes |
|
