Sample Set Annotation Tool: Effect of maternal tobacco smoke exposure on the placental transcriptome

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Smoking in pregnancy increases a woman's risk of preterm delivery resulting in serious health problems during the newborn period, chronic lifelong disabilities (such as cerebral palsy, mental retardation and learning problems), and even death. Further, smoking women have placental problems such as placenta previa (a low-lying placenta that covers part or all of the opening of the uterus), placental abruption (in which the placenta peels away, partially or almost completely before delivery) often resulting in bleeding during delivery. Gene expression profiles in placentas from women exposed to tobacco smoke in pregnancy and from those without the exposure were determined by Illumina HumRef8 Beadchips with 20,589 gene probes. Comparative analysis, smokers versus non-smokers, revealed differential expression of 241 genes at p<0.05. In smokers we identified deregulated genes that represent general biomarkers of exposure as well as candidate genes likely involved in placental abnormalities found in smoking women. Functional annotation determined deregulated processes that were mainly related to development, metabolism, ion transport, and adhesion.

Hypothesis

Experimental Design

The study comprised 76 women who gave birth to a baby at the Children Hospital of Motol in Prague. All participants provided written informed consent and filled in the questionnaire including information about their smoking history in pregnancy, life style, pregnancy history, delivery course and newborn characteristics. To study effect of tobacco smoke on placental transcriptome, we performed gene expression profiling in placentas from women exposed to tobacco smoke in pregnancy (N=12) and from those without the exposure (N=64).

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

76 Samples Loaded: 76

Species

Human (Homo sapiens)

Sample Source

placenta

Disease

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	parity	!Sample Title	Age (years)	Gestational age (weeks)	Maternal bmi
GSM451162	1	non-smoker 101	32	39	25.7
GSM451163	1	non-smoker 102	28	37	18.8
GSM451164	2	non-smoker 103	38	36	21.3
GSM451165	3	non-smoker 104	34	41	23.5
GSM451166	2	light smoker 105	27	42	22

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File
sampleset4000020_sampleannotations_group.csv Sample Set Spreadsheet
sampleset4000020_sampleannotations_group.csv Sample Set Spreadsheet
sampleset4000020_sampleannotations_group.csv Sample Set Spreadsheet
sampleset4000020_sampleannotations_original.csv Sample Set Spreadsheet

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Sample ID	Parity	!Sample Title	Age (years)	Gestational age (weeks)	Maternal bmi	Mode of delivery	Group	Placental volume (cm3)	Status
GSM451162	1	non-smoker 101	32	39	25.7	vaginal	non-smoker	1000	non-smoker
GSM451163	1	non-smoker 102	28	37	18.8	vaginal	non-smoker	1200	non-smoker
GSM451164	2	non-smoker 103	38	36	21.3	caesarean	non-smoker	1200	non-smoker
GSM451165	3	non-smoker 104	34	41	23.5	vaginal	non-smoker	1800	non-smoker
GSM451166	2	light smoker 105	27	42	22	vaginal	smoker	1800	smoker
GSM451167	2	non-smoker 106	31	39	31.8	vaginal	non-smoker	1200	non-smoker
GSM451168	1	non-smoker 107	31	39	25.6	vaginal	non-smoker	600	non-smoker
GSM451169	1	non-smoker 108	32	39	19.8	vaginal	non-smoker	855	non-smoker
GSM451170	2	non-smoker 109	32	41	18.6	vaginal	non-smoker	900	non-smoker
GSM451171	3	non-smoker 110	33	41	23.7	vaginal	non-smoker	1200	non-smoker
GSM451172	2	non-smoker 111	32	41	21.5	vaginal	non-smoker	675	non-smoker
GSM451173	1	non-smoker 112	27	40	19.7	vaginal	non-smoker	1020	non-smoker
GSM451174	1	non-smoker 113	35	39	28.4	vaginal	non-smoker	1200	non-smoker
GSM451175	2	non-smoker 114	37	41	26.8	vaginal	non-smoker	880	non-smoker
GSM451176	1	heavy smoker 115	24	37	30.8	vaginal	smoker	2500	smoker
GSM451177	1	non-smoker 116	34	39	21.3	caesarean	non-smoker	1200	non-smoker
GSM451178	2	non-smoker 117	35	40	24.6	vaginal	non-smoker	1725	non-smoker
GSM451179	2	non-smoker 118	33	42	19.4	vaginal	non-smoker	1320	non-smoker
GSM451180	2	non-smoker 119	33	38	20.8	vaginal	non-smoker	1320	non-smoker
GSM451181	3	non-smoker 120	38	40	15.9	vaginal	non-smoker	1080	non-smoker
GSM451182	2	non-smoker 121	35	40	20.7	vaginal	non-smoker	867	non-smoker
GSM451183	1	non-smoker 122	28	39	26.1	vaginal	non-smoker	720	non-smoker
GSM451184	5	non-smoker 123	39	38	19.7	vaginal	non-smoker	675	non-smoker
GSM451185	4	non-smoker 124	37	41	26	vaginal	non-smoker	3150	non-smoker
GSM451186	1	non-smoker 125	34	39	25.9	vaginal	non-smoker	792	non-smoker
GSM451187	1	non-smoker 126	28	38	24	vaginal	non-smoker	1200	non-smoker
GSM451188	3	non-smoker 127	35	39	21.6	vaginal	non-smoker	540	non-smoker
GSM451189	2	non-smoker 128	34	41	25	vaginal	non-smoker	648	non-smoker
GSM451190	2	non-smoker 129	33	39	24.6	vaginal	non-smoker	2500	non-smoker
GSM451191	2	non-smoker 130	33	38	24.7	vaginal	non-smoker	720	non-smoker
GSM451192	5	heavy smoker 131	23	40	19.1	vaginal	smoker	1500	smoker
GSM451193	2	non-smoker 132	28	39	24.4	vaginal	non-smoker	1000	non-smoker
GSM451194	4	light smoker 133	36	41	24	vaginal	smoker	1080	smoker
GSM451195	1	non-smoker 134	23	39	16.4	vaginal	non-smoker	1500	non-smoker
GSM451196	2	non-smoker 135	38	39	21.4	vaginal	non-smoker	1200	non-smoker
GSM451197	1	non-smoker 136	32	39	21.2	vaginal	non-smoker	2500	non-smoker
GSM451198	5	light smoker 137	29	38	28.1	caesarean	smoker	765	smoker
GSM451199	3	non-smoker 138	37	39	34.9	vaginal	non-smoker	800	non-smoker
GSM451200	2	heavy smoker 139	24	41	32.2	vaginal	smoker	800	smoker
GSM451201	1	non-smoker 140	31	40	23.5	caesarean	non-smoker	1500	non-smoker
GSM451202	1	non-smoker 141	29	39	21	vaginal	non-smoker	1200	non-smoker
GSM451203	3	non-smoker 142	27	37	19.4	vaginal	non-smoker	1650	non-smoker
GSM451204	2	non-smoker 143	34	42	22.4	vaginal	non-smoker	660	non-smoker
GSM451205	3	non-smoker 144	29	37	25.5	vaginal	non-smoker	720	non-smoker
GSM451206	2	non-smoker 145	37	39	20.4	vaginal	non-smoker	748	non-smoker
GSM451207	1	non-smoker 146	33	40	23.1	vaginal	non-smoker	480	non-smoker
GSM451208	1	non-smoker 147	32	41	23.7	vaginal	non-smoker	646	non-smoker
GSM451209	1	non-smoker 148	28	42	23.3	caesarean	non-smoker	1449	non-smoker
GSM451210	2	non-smoker 149	41	40	not available	vaginal	non-smoker	680	non-smoker
GSM451211	1	heavy smoker 150	34	36	19.5	vaginal	smoker	1000	smoker
GSM451212	1	non-smoker 151	33	37	23.8	caesarean	non-smoker	960	non-smoker
GSM451213	1	non-smoker 152	32	39	19.7	vaginal	non-smoker	765	non-smoker
GSM451214	1	non-smoker 153	27	39	21	vaginal	non-smoker	1020	non-smoker
GSM451215	1	non-smoker 154	31	39	22.7	vaginal	non-smoker	600	non-smoker
GSM451216	1	non-smoker 155	28	40	18.6	vaginal	non-smoker	336	non-smoker
GSM451217	1	non-smoker 156	29	36	19.8	vaginal	non-smoker	1386	non-smoker
GSM451218	1	light smoker 157	27	39	28	vaginal	smoker	510	smoker
GSM451219	1	non-smoker 158	32	39	21	vaginal	non-smoker	1200	non-smoker
GSM451220	3	non-smoker 159	36	38	23.7	vaginal	non-smoker	1020	non-smoker
GSM451221	1	non-smoker 160	29	39	20	caesarean	non-smoker	1026	non-smoker
GSM451222	4	non-smoker 161	40	35	20.4	vaginal	non-smoker	1518	non-smoker
GSM451223	1	heavy smoker 162	22	41	34.1	vaginal	smoker	800	smoker
GSM451224	not available	non-smoker 163	not available	not available	not available	not avalaible	non-smoker	544	non-smoker
GSM451225	1	non-smoker 164	33	38	19.7	vaginal	non-smoker	1260	non-smoker
GSM451226	4	non-smoker 166	40	40	25.1	vaginal	non-smoker	1150	non-smoker
GSM451227	2	non-smoker 167	37	38	20.9	vaginal	non-smoker	2700	non-smoker
GSM451228	2	non-smoker 168	42	41	27.9	vaginal	non-smoker	2400	non-smoker
GSM451229	2	heavy smoker 170	27	37	24.1	vaginal	smoker	972	smoker
GSM451230	1	non-smoker 171	30	41	24.4	vaginal	non-smoker	1725	non-smoker
GSM451231	5	non-smoker 173	46	40	27.4	vaginal	non-smoker	840	non-smoker
GSM451232	2	light smoker 174	25	41	18.6	caesarean	smoker	1380	smoker
GSM451233	7	non-smoker 175	34	38	22.9	vaginal	non-smoker	972	non-smoker
GSM451234	3	non-smoker 176	34	39	21.5	vaginal	non-smoker	1725	non-smoker
GSM451235	1	non-smoker 177	33	40	33.9	vaginal	non-smoker	1150	non-smoker
GSM451236	4	non-smoker 178	38	39	25.6	vaginal	non-smoker	600	non-smoker
GSM451237	1	heavy smoker 179	23	40	19	vaginal	smoker	1320	smoker

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