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Sample GSM3151786 Query DataSets for GSM3151786
Status Public on May 25, 2018
Title Sample100: Umbilical cord blood - Control
Sample type RNA
Source name Umbilical cord blood
Organism Homo sapiens
Characteristics tissue: Umbilical cord blood
maternal diagnosis: Control
neonate gender: Male
rin: 8.6
microarray batch: One
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

Data table header descriptions
VALUE The neqc function of limma was used to normalize all data.
SAMPLE100 DetectionPval

Data table
ID_REF VALUE SAMPLE100 DetectionPval
ILMN_1343291 12.3957 0
ILMN_1343295 7.7907 0
ILMN_1651229 4.4215 0.2169
ILMN_1651254 5.2103 0.0143
ILMN_1651259 4.5328 0.0805
ILMN_1651262 5.581 0.0091
ILMN_1651279 5.3617 0.0117
ILMN_1651282 4.489 0.1156
ILMN_1651288 6.2663 0.0065
ILMN_1651315 6.1915 0.0065
ILMN_1651316 4.3416 0.5013
ILMN_1651328 4.8042 0.0312
ILMN_1651346 4.6809 0.0429
ILMN_1651347 5.2258 0.0143
ILMN_1651373 6.1995 0.0065
ILMN_1651378 4.83 0.0299
ILMN_1651385 4.7641 0.0325
ILMN_1651403 4.4661 0.139
ILMN_1651405 4.7425 0.0338
ILMN_1651433 7.4338 0

Total number of rows: 13405

Table truncated, full table size 343 Kbytes.

Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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