Sample Set Annotation Tool: Differentially expressed mRNA transcripts in the placenta delivered by preterm versus term spontaneous labour

Study Design
Assay
Sample Info
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Analysis

Purpose

We hypothesized that preterm spontaneous labor involves aberrant changes in mRNA expression in the placenta. To test this hypothesis, we interrogated the mRNA levels of >50,000 genes and transcript variants using gene expression microarray (Human Genome U133 Plus 2.0 Array, Affymetrix) on 5 placentas collected from preterm spontaneous delivery (<34 weeks of gestation) and another 5 placentas collected from term spontaneous delivery (38-39 weeks).We have identified 229 and 162 genes that were up- or down-regulated, respectively, for more than 3-fold in the preterm placentas compared to the term placentas (Mann-Whitney Rank Sum Test, with multiple testing correction by the Benjamini-Hochberg method, adjusted p-value <= 0.05).

Hypothesis

Experimental Design

Placentas collected from (i) preterm spontaneous delivery (<34 weeks of gestation) and (ii) term spontaneous delivery (38-39 weeks of gestation) were subjected to RNA extraction and hybridization on Affymetrix microarrays. To identify gene expression patterns that are commonly involved in preterm spontaneous labour, we analyzed 5 placentas from each of these 2 groups and tested for any differentially expressed genes by Mann-Whitney Rank Sum Test.

Experimental Variables

Controls

Methods

Additional Information

Expected Samples:

10 Samples Loaded: 10

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	tissue	!Sample Title	Group	Delivery location	Developmental stage
GSM466504	placenta	Placenta, Preterm spontaneous delivery, Biological Replicate #1	preterm	Prince of Wales Hospital, Hong Kong	preterm spontaneous delivery (<34 weeks of gestation)
GSM466505	placenta	Placenta, Preterm spontaneous delivery, Biological Replicate #2	preterm	Prince of Wales Hospital, Hong Kong	preterm spontaneous delivery (<34 weeks of gestation)
GSM466506	placenta	Placenta, Preterm spontaneous delivery, Biological Replicate #3	preterm	Prince of Wales Hospital, Hong Kong	preterm spontaneous delivery (<34 weeks of gestation)
GSM466507	placenta	Placenta, Preterm spontaneous delivery, Biological Replicate #4	preterm	Prince of Wales Hospital, Hong Kong	preterm spontaneous delivery (<34 weeks of gestation)
GSM466508	placenta	Placenta, Preterm spontaneous delivery, Biological Replicate #5	preterm	Prince of Wales Hospital, Hong Kong	preterm spontaneous delivery (<34 weeks of gestation)

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sampleset4000030_sampleannotations_group.csv Sample Set Spreadsheet
sampleset4000030_sampleannotations_group.csv Sample Set Spreadsheet

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Sample ID	Tissue	!Sample Title	Group	Delivery location	Developmental stage	Maternal ethnicity
GSM466504	placenta	Placenta, Preterm spontaneous delivery, Biological Replicate #1	preterm	Prince of Wales Hospital, Hong Kong	preterm spontaneous delivery (<34 weeks of gestation)	Chinese
GSM466505	placenta	Placenta, Preterm spontaneous delivery, Biological Replicate #2	preterm	Prince of Wales Hospital, Hong Kong	preterm spontaneous delivery (<34 weeks of gestation)	Chinese
GSM466506	placenta	Placenta, Preterm spontaneous delivery, Biological Replicate #3	preterm	Prince of Wales Hospital, Hong Kong	preterm spontaneous delivery (<34 weeks of gestation)	Chinese
GSM466507	placenta	Placenta, Preterm spontaneous delivery, Biological Replicate #4	preterm	Prince of Wales Hospital, Hong Kong	preterm spontaneous delivery (<34 weeks of gestation)	Chinese
GSM466508	placenta	Placenta, Preterm spontaneous delivery, Biological Replicate #5	preterm	Prince of Wales Hospital, Hong Kong	preterm spontaneous delivery (<34 weeks of gestation)	Chinese
GSM466509	placenta	Placenta, Term spontaneous delivery, Biological Replicate #1	term	Prince of Wales Hospital, Hong Kong	term spontaneous delivery (38-39 weeks of gestation)	Chinese
GSM466510	placenta	Placenta, Term spontaneous delivery, Biological Replicate #2	term	Prince of Wales Hospital, Hong Kong	term spontaneous delivery (38-39 weeks of gestation)	Chinese
GSM466511	placenta	Placenta, Term spontaneous delivery, Biological Replicate #3	term	Prince of Wales Hospital, Hong Kong	term spontaneous delivery (38-39 weeks of gestation)	Chinese
GSM466512	placenta	Placenta, Term spontaneous delivery, Biological Replicate #4	term	Prince of Wales Hospital, Hong Kong	term spontaneous delivery (38-39 weeks of gestation)	Chinese
GSM466513	placenta	Placenta, Term spontaneous delivery, Biological Replicate #5	term	Prince of Wales Hospital, Hong Kong	term spontaneous delivery (38-39 weeks of gestation)	Chinese

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