A database of the human placenta transcriptome

This is a Shiny web application to browse the human placenta transcriptome based on the POP study.

It is developed and maintained by the Department of Obstetrics & Gynaecology

School of Clinical Medicine

University of Cambridge

University of Cambridge

Select differentially expressed genes by a statistical significance level (p-value)
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Select differentially expressed genes within top 5% fold-change calculated by bootstrapping of samples 5000 times
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Search DEGs by gene names(s) HGNC
Search DEGs by Ensembl ID(s)
Browse the transcript abundance level
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Browse transcripts enriched in the placenta
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Tissue-wide comparision of expression level
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Dalliance goes here...

TrackHub to visualize from the UCSC genome browser

The hub file is avaible from here if you would like to visualize our data from the UCSC Trac Hub.

Or you can simply follow this link.

Below shows a genome browser embeded image highlighting circSTS.

The POP (Pregancny Outcome Prediction) Study

The POPs study included 4,512 nulliparous women with a viable singleton pregnancy attending The Rosie Hospital (Cambridge, UK) for their dating ultrasound scan between 2008 and 2012 (Pasupathy et al 2008, Gaccioli et al 2016). Women were serially scanned through the pregnancy and had blood obtained at recruitment, 20, 28 and 36 weeks gestational age. DNA samples and height/weight measurements of the partners were also collected. After delivery, biopsies of the placenta, placental membranes, umbilical cord, and cord blood were collected. Thorough design of POPs and careful sample collection allowed us to create an extensive, optimally phenotyped biobank of complicated pregnancies and controls, including approximately 230,000 blood and tissue samples stored in -80°C freezers, 24,000 formalin fixed placental biopsies, and 4,000 paternal DNA samples. Read more here.

Placenta Samples

All the samples were obtained from the Pregnancy Outcome Prediction Study (POPS) – a prospective cohort study of nulliparous women attending the Rosie Hospital, Cambridge (UK) for their dating ultrasound scan between January 14, 2008, and July 31, 2012.

A total of 302 unique placenta samples were considered in this study, among which there were 94 PE, 56 FGR, and 155 control samples – three cases of samples were classified as both PE and FGR.

We generated 324 total RNA-Seq data sets from 302 unique placental biopsies – 22 biopsies were sequenced twice (19 control samples and 3 samples classified as both PE and FGR cases).

Out of the 302 placental biopsies, three samples were excluded due to the presence of decidual contamination of the placental biopsies.

Three cases (i.e. samples classified as both PE and FGR) were also excluded in the analyses (except differentially expressed gene analysis).

A further sample was flagged as failed at the library preparation process.

Thus, a total of 295 unique placental biopsies were used (159 male and 136 female placentas).

Annotations Used

GRCh38.p3

Ensembl 82

miRBase v21

piRBase v1.0

Acknowledgement

This project is fully funded by the NIHR Cambridge Biomedical Research Centre

Disclaimer

The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care.

Reference

Under review…

Availability

The source code is available here

RNA-seq data have been deposited in the European genome-phenome archive, with an accession number EGAS00001002205.


Developed and maintained by Sung Gong

University of Cambridge