Sample Set Annotation Tool: The role of vitamin D in the transcriptional program of human pregnancy-GSE86200

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Peripheral whole blood transcriptome profiles of pregnant women enrolled in the “Vitamin D Antenatal Asthma Reduction Trial” (VDAART) at enrollment during early pregnancy, and again at 32-38 weeks of gestation. Mothers were enrolled in 2 treatment groups: Intervention group with 4400 IU vitamin D supplementation and Control group with 400 IU vitamin D supplementation.Comparing the whole blood (PAXgene) transcriptome profile of 30 mothers at enrollment during early pregnancy versus their matching individual profile at 32-38 weeks of gestation.

Hypothesis

Experimental Design

Whole blood transcriptome, dose response, time course, matched pair analysis

Experimental Variables

Controls

Methods

All 60 samples were standard background adjusted, logarithm base 2 transformed and quantile normalized using the R Bioconductor package lumi. Gene probes with empty gene symbols or unspecified chromosome locations were remove beforehand.

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86200

Expected Samples:

60 Samples Loaded: 60

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

Pregnancy

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

Please log in in order to upload files.

Samples Preview

Sample ID	Ethnicity	!Sample_title	tissue	Sex	age at enrollment
GSM2297636	Caucasian (Non-Hispanic)	8082231-M, at enrollment	PAXgene whole blood	Female	25.83709788
GSM2297637	Caucasian (Non-Hispanic)	8082231-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	25.83709788
GSM2297638	African American (Hispanic and Non-Hispanic)	2093964-M, at enrollment	PAXgene whole blood	Female	18.89390828
GSM2297639	African American (Hispanic and Non-Hispanic)	2093964-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	18.89390828
GSM2297640	African American (Hispanic and Non-Hispanic)	2066267-M, at enrollment	PAXgene whole blood	Female	29.68925394

Please log in in order to upload files.

File

Samples Viewer / Editor

All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.

Sample ID	Ethnicity	!Sample Title	Tissue	Sex	Age at enrollment	Treatment group	Recruitment ID	Vitamin d level at enrollment (nmol/l)	Pregnancy condition	Gestational day at enrollment	Vitamin d level at 32-38 weeks of gestation (nmol/l)	Study center	Microarray hybridization date	Sex of child
GSM2297636	Caucasian (Non-Hispanic)	8082231-M, at enrollment	PAXgene whole blood	Female	25.83709788	Intervention group, 4400 IU vitamin D supplementation	8082231-M	95.25	Normal	129	96.5	KP - Kaiser Permanente	05/23/2012	Female
GSM2297637	Caucasian (Non-Hispanic)	8082231-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	25.83709788	Intervention group, 4400 IU vitamin D supplementation	8082231-M	95.25	Normal	129	96.5	KP - Kaiser Permanente	02/27/2012	Female
GSM2297638	African American (Hispanic and Non-Hispanic)	2093964-M, at enrollment	PAXgene whole blood	Female	18.89390828	Intervention group, 4400 IU vitamin D supplementation	2093964-M	111.5	Normal	108	120.25	KP - Kaiser Permanente	02/27/2012	Female
GSM2297639	African American (Hispanic and Non-Hispanic)	2093964-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	18.89390828	Intervention group, 4400 IU vitamin D supplementation	2093964-M	111.5	Normal	108	120.25	KP - Kaiser Permanente	02/27/2012	Female
GSM2297640	African American (Hispanic and Non-Hispanic)	2066267-M, at enrollment	PAXgene whole blood	Female	29.68925394	Intervention group, 4400 IU vitamin D supplementation	2066267-M	80.25	Normal	127	136.9	KP - Kaiser Permanente	02/27/2012	Female
GSM2297641	African American (Hispanic and Non-Hispanic)	2066267-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	29.68925394	Intervention group, 4400 IU vitamin D supplementation	2066267-M	80.25	Normal	127	136.9	KP - Kaiser Permanente	02/27/2012	Female
GSM2297642	African American (Hispanic and Non-Hispanic)	9061441-M, at enrollment	PAXgene whole blood	Female	19.86310746	Control group, 400 IU vitamin D supplementation	9061441-M	55	Normal	113	48.25	KP - Kaiser Permanente	05/23/2012	Female
GSM2297643	African American (Hispanic and Non-Hispanic)	9061441-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	19.86310746	Control group, 400 IU vitamin D supplementation	9061441-M	55	Normal	113	48.25	KP - Kaiser Permanente	02/27/2012	Female
GSM2297644	Caucasian (Non-Hispanic)	1027224-M, at enrollment	PAXgene whole blood	Female	33.48117728	Intervention group, 4400 IU vitamin D supplementation	1027224-M	93.75	Normal	108	138.75	KP - Kaiser Permanente	02/27/2012	Male
GSM2297645	Caucasian (Non-Hispanic)	1027224-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	33.48117728	Intervention group, 4400 IU vitamin D supplementation	1027224-M	93.75	Normal	108	138.75	KP - Kaiser Permanente	02/27/2012	Male
GSM2297646	Caucasian (Non-Hispanic)	6041552-M, at enrollment	PAXgene whole blood	Female	28.48733744	Intervention group, 4400 IU vitamin D supplementation	6041552-M	49	Normal	88	83	KP - Kaiser Permanente	02/27/2012	Male
GSM2297647	Caucasian (Non-Hispanic)	6041552-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	28.48733744	Intervention group, 4400 IU vitamin D supplementation	6041552-M	49	Normal	88	83	KP - Kaiser Permanente	02/27/2012	Male
GSM2297648	African American (Hispanic and Non-Hispanic)	1044556-M, at enrollment	PAXgene whole blood	Female	30.34086242	Control group, 400 IU vitamin D supplementation	1044556-M	53.75	Normal	90	65.75	BU - Boston University	02/27/2012	Female
GSM2297649	African American (Hispanic and Non-Hispanic)	1044556-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	30.34086242	Control group, 400 IU vitamin D supplementation	1044556-M	53.75	Normal	90	65.75	BU - Boston University	02/27/2012	Female
GSM2297650	African American (Hispanic and Non-Hispanic)	5025572-M, at enrollment	PAXgene whole blood	Female	22.36276523	Control group, 400 IU vitamin D supplementation	5025572-M	36.75	Normal	129	58.5	BU - Boston University	02/27/2012	Female
GSM2297651	African American (Hispanic and Non-Hispanic)	5025572-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	22.36276523	Control group, 400 IU vitamin D supplementation	5025572-M	36.75	Normal	129	58.5	BU - Boston University	02/27/2012	Female
GSM2297652	African American (Hispanic and Non-Hispanic)	5037279-M, at enrollment	PAXgene whole blood	Female	20.88980151	Control group, 400 IU vitamin D supplementation	5037279-M	43.25	Preeclampsia	127	49.5	BU - Boston University	02/27/2012	Male
GSM2297653	African American (Hispanic and Non-Hispanic)	5037279-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	20.88980151	Control group, 400 IU vitamin D supplementation	5037279-M	43.25	Preeclampsia	127	49.5	BU - Boston University	02/27/2012	Male
GSM2297654	African American (Hispanic and Non-Hispanic)	4041035-M, at enrollment	PAXgene whole blood	Female	28.34223135	Intervention group, 4400 IU vitamin D supplementation	4041035-M	63	Normal	85	142.5	BU - Boston University	05/23/2012	Female
GSM2297655	African American (Hispanic and Non-Hispanic)	4041035-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	28.34223135	Intervention group, 4400 IU vitamin D supplementation	4041035-M	63	Normal	85	142.5	BU - Boston University	02/27/2012	Female
GSM2297656	Caucasian (Non-Hispanic)	2006605-M, at enrollment	PAXgene whole blood	Female	33.61533196	Control group, 400 IU vitamin D supplementation	2006605-M	65.5	Normal	92	91.25	BU - Boston University	02/27/2012	Female
GSM2297657	Caucasian (Non-Hispanic)	2006605-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	33.61533196	Control group, 400 IU vitamin D supplementation	2006605-M	65.5	Normal	92	91.25	BU - Boston University	02/27/2012	Female
GSM2297658	African American (Hispanic and Non-Hispanic)	1086584-M, at enrollment	PAXgene whole blood	Female	36.77207392	Control group, 400 IU vitamin D supplementation	1086584-M	34.25	Normal	90	39.5	BU - Boston University	02/27/2012	Female
GSM2297659	African American (Hispanic and Non-Hispanic)	1086584-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	36.77207392	Control group, 400 IU vitamin D supplementation	1086584-M	34.25	Normal	90	39.5	BU - Boston University	02/27/2012	Female
GSM2297660	Caucasian (Non-Hispanic)	2067862-M, at enrollment	PAXgene whole blood	Female	25.19096509	Control group, 400 IU vitamin D supplementation	2067862-M	89	Normal	85	91	WU - Washington University	02/27/2012	Male
GSM2297661	Caucasian (Non-Hispanic)	2067862-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	25.19096509	Control group, 400 IU vitamin D supplementation	2067862-M	89	Normal	85	91	WU - Washington University	02/27/2012	Male
GSM2297662	African American (Hispanic and Non-Hispanic)	3045067-M, at enrollment	PAXgene whole blood	Female	30.72416153	Intervention group, 4400 IU vitamin D supplementation	3045067-M	25.5	Preeclampsia	89	56.5	WU - Washington University	02/27/2012	Male
GSM2297663	African American (Hispanic and Non-Hispanic)	3045067-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	30.72416153	Intervention group, 4400 IU vitamin D supplementation	3045067-M	25.5	Preeclampsia	89	56.5	WU - Washington University	02/27/2012	Male
GSM2297664	African American (Hispanic and Non-Hispanic)	4001301-M, at enrollment	PAXgene whole blood	Female	20.62422998	Intervention group, 4400 IU vitamin D supplementation	4001301-M	40.75	Normal	115	94	WU - Washington University	02/27/2012	Male
GSM2297665	African American (Hispanic and Non-Hispanic)	4001301-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	20.62422998	Intervention group, 4400 IU vitamin D supplementation	4001301-M	40.75	Normal	115	94	WU - Washington University	02/27/2012	Male
GSM2297666	African American (Hispanic and Non-Hispanic)	3012659-M, at enrollment	PAXgene whole blood	Female	20.54757016	Intervention group, 4400 IU vitamin D supplementation	3012659-M	37.75	Preeclampsia	85	157	WU - Washington University	02/27/2012	Male
GSM2297667	African American (Hispanic and Non-Hispanic)	3012659-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	20.54757016	Intervention group, 4400 IU vitamin D supplementation	3012659-M	37.75	Preeclampsia	85	157	WU - Washington University	02/27/2012	Male
GSM2297668	African American (Hispanic and Non-Hispanic)	6057756-M, at enrollment	PAXgene whole blood	Female	32.8514716	Intervention group, 4400 IU vitamin D supplementation	6057756-M	21.675	Normal	70	125.5	WU - Washington University	02/27/2012	Male
GSM2297669	African American (Hispanic and Non-Hispanic)	6057756-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	32.8514716	Intervention group, 4400 IU vitamin D supplementation	6057756-M	21.675	Normal	70	125.5	WU - Washington University	02/27/2012	Male
GSM2297670	African American (Hispanic and Non-Hispanic)	4031682-M, at enrollment	PAXgene whole blood	Female	19.8384668	Control group, 400 IU vitamin D supplementation	4031682-M	18.2	Normal	72	23.05	WU - Washington University	05/23/2012	Female
GSM2297671	African American (Hispanic and Non-Hispanic)	4031682-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	19.8384668	Control group, 400 IU vitamin D supplementation	4031682-M	18.2	Normal	72	23.05	WU - Washington University	02/27/2012	Female
GSM2297672	African American (Hispanic and Non-Hispanic)	1086430-M, at enrollment	PAXgene whole blood	Female	22.17659138	Control group, 400 IU vitamin D supplementation	1086430-M	28.25	Preeclampsia	72	37.25	WU - Washington University	02/27/2012	Male
GSM2297673	African American (Hispanic and Non-Hispanic)	1086430-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	22.17659138	Control group, 400 IU vitamin D supplementation	1086430-M	28.25	Preeclampsia	72	37.25	WU - Washington University	02/27/2012	Male
GSM2297674	African American (Hispanic and Non-Hispanic)	9028555-M, at enrollment	PAXgene whole blood	Female	18.02327173	Intervention group, 4400 IU vitamin D supplementation	9028555-M	36.5	Normal	98	95.75	WU - Washington University	02/27/2012	Female
GSM2297675	African American (Hispanic and Non-Hispanic)	9028555-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	18.02327173	Intervention group, 4400 IU vitamin D supplementation	9028555-M	36.5	Normal	98	95.75	WU - Washington University	02/27/2012	Female
GSM2297676	African American (Hispanic and Non-Hispanic)	4018451-M, at enrollment	PAXgene whole blood	Female	18.27789186	Control group, 400 IU vitamin D supplementation	4018451-M	43.25	Normal	102	39	WU - Washington University	02/27/2012	Female
GSM2297677	African American (Hispanic and Non-Hispanic)	4018451-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	18.27789186	Control group, 400 IU vitamin D supplementation	4018451-M	43.25	Normal	102	39	WU - Washington University	02/27/2012	Female
GSM2297678	African American (Hispanic and Non-Hispanic)	2067143-M, at enrollment	PAXgene whole blood	Female	27.91238878	Intervention group, 4400 IU vitamin D supplementation	2067143-M	21.3	Normal	112	80.25	WU - Washington University	02/27/2012	Female
GSM2297679	African American (Hispanic and Non-Hispanic)	2067143-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	27.91238878	Intervention group, 4400 IU vitamin D supplementation	2067143-M	21.3	Normal	112	80.25	WU - Washington University	02/27/2012	Female
GSM2297680	African American (Hispanic and Non-Hispanic)	8057224-M, at enrollment	PAXgene whole blood	Female	18.13278576	Control group, 400 IU vitamin D supplementation	8057224-M	30.75	Normal	124	63.5	WU - Washington University	02/27/2012	Male
GSM2297681	African American (Hispanic and Non-Hispanic)	8057224-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	18.13278576	Control group, 400 IU vitamin D supplementation	8057224-M	30.75	Normal	124	63.5	WU - Washington University	05/23/2012	Male
GSM2297682	African American (Hispanic and Non-Hispanic)	6058718-M, at enrollment	PAXgene whole blood	Female	20.91444216	Control group, 400 IU vitamin D supplementation	6058718-M	46.25	Normal	75	90.25	WU - Washington University	02/27/2012	Male
GSM2297683	African American (Hispanic and Non-Hispanic)	6058718-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	20.91444216	Control group, 400 IU vitamin D supplementation	6058718-M	46.25	Normal	75	90.25	WU - Washington University	05/23/2012	Male
GSM2297684	African American (Hispanic and Non-Hispanic)	5098874-M, at enrollment	PAXgene whole blood	Female	22.49965777	Control group, 400 IU vitamin D supplementation	5098874-M	34	Preeclampsia	82	54	WU - Washington University	05/23/2012	Female
GSM2297685	African American (Hispanic and Non-Hispanic)	5098874-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	22.49965777	Control group, 400 IU vitamin D supplementation	5098874-M	34	Preeclampsia	82	54	WU - Washington University	02/27/2012	Female
GSM2297686	Caucasian (Non-Hispanic)	7052439-M, at enrollment	PAXgene whole blood	Female	32.38603696	Control group, 400 IU vitamin D supplementation	7052439-M	49.125	Normal	94	60.75	WU - Washington University	02/27/2012	Male
GSM2297687	Caucasian (Non-Hispanic)	7052439-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	32.38603696	Control group, 400 IU vitamin D supplementation	7052439-M	49.125	Normal	94	60.75	WU - Washington University	02/27/2012	Male
GSM2297688	African American (Hispanic and Non-Hispanic)	3095286-M, at enrollment	PAXgene whole blood	Female	18.60643395	Control group, 400 IU vitamin D supplementation	3095286-M	60.5	Normal	76	110.75	WU - Washington University	02/27/2012	Male
GSM2297689	African American (Hispanic and Non-Hispanic)	3095286-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	18.60643395	Control group, 400 IU vitamin D supplementation	3095286-M	60.5	Normal	76	110.75	WU - Washington University	02/27/2012	Male
GSM2297690	African American (Hispanic and Non-Hispanic)	3019680-M, at enrollment	PAXgene whole blood	Female	27.05817933	Intervention group, 4400 IU vitamin D supplementation	3019680-M	17.55	Normal	106	33.75	WU - Washington University	02/27/2012	Female
GSM2297691	African American (Hispanic and Non-Hispanic)	3019680-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	27.05817933	Intervention group, 4400 IU vitamin D supplementation	3019680-M	17.55	Normal	106	33.75	WU - Washington University	02/27/2012	Female
GSM2297692	African American (Hispanic and Non-Hispanic)	7063614-M, at enrollment	PAXgene whole blood	Female	29.229295	Intervention group, 4400 IU vitamin D supplementation	7063614-M	16.075	Preeclampsia	98	27	WU - Washington University	02/27/2012	Male
GSM2297693	African American (Hispanic and Non-Hispanic)	7063614-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	29.229295	Intervention group, 4400 IU vitamin D supplementation	7063614-M	16.075	Preeclampsia	98	27	WU - Washington University	02/27/2012	Male
GSM2297694	African American (Hispanic and Non-Hispanic)	5028464-M, at enrollment	PAXgene whole blood	Female	23.06913073	Intervention group, 4400 IU vitamin D supplementation	5028464-M	21.2	Normal	100	62	WU - Washington University	02/27/2012	Male
GSM2297695	African American (Hispanic and Non-Hispanic)	5028464-M, at 32-38 weeks of gestation	PAXgene whole blood	Female	23.06913073	Intervention group, 4400 IU vitamin D supplementation	5028464-M	21.2	Normal	100	62	WU - Washington University	02/27/2012	Male

Group Sets View in Gene Expression Browser

Name
All Samples	Default	View
In order to make new Group Sets or change settings, please log in.

Module Analysis

Group Set
All Samples

SIDRA