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Open Access Highly Accessed Research article

Transcriptome landscape of the human placenta

Jinsil Kim1, Keyan Zhao2, Peng Jiang2, Zhi-xiang Lu2, Jinkai Wang2, Jeffrey C Murray345* and Yi Xing267*

Author Affiliations

1 Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA

2 Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA

3 Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA

4 Department of Biology, University of Iowa, Iowa City, IA 52242, USA

5 Department of Epidemiology, University of Iowa, Iowa City, IA 52242, USA

6 Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242, USA

7 Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA

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BMC Genomics 2012, 13:115  doi:10.1186/1471-2164-13-115

Published: 27 March 2012

Additional files

Additional file 1:

Tables S1 and S2 and Figures S1-3 Supplemental Table S1. Mapping statistics of RNA-Seq data from placenta and HBM2.0 tissues. Supplemental Table S2. Distribution of gene expression level (FPKM) of RNA-Seq data from placenta and HBM2.0 tissues. Figure S1. Distribution of gene expression values (FPKM) for all tissues examined in the study. Figure S2. qRT-PCR validation of placenta-enriched SFs ESRP1 and MBNL3. Figure S3. Functional interaction network analysis of genes with enriched expression (EE) and differential splicing (DS) that intersect all three placental tissues: module 2. Circular node: a query gene. Diamond-shaped node: a linker gene. Node color was determined based on whether the query gene shows EE (green), DS (pink), or both (red). The most significantly enriched pathways were highlighted in bigger node size: integrin signaling pathway and ECM-receptor interaction pathway.

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Additional file 2:

Table S3 Enriched pathways (FDR < 0.05) in the whole network and submodules (module size > 50) from functional interaction network analysis.

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Additional file 3:

Table S4 FPKM expression levels in all tissues for the novel TARs identified from the placental tissues.

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Additional file 4:

Table S5 Exon inclusion levels and primer sequences for exons selected for RT-PCR validation.

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Additional file 5:

Figure S4 RT-PCR analysis of 34 exons that showed significant differential splicing (> 10% difference in exon inclusion level, FDR < 0.1) between placental and HBM2.0 tissues. Figure S5. RT-PCR analysis of 21 ESRP1target exons.

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