Description
Display Conventions and Configuration
These bed tracks show replicated bins for each tissue type. Only replicated bins are drawn and they are only coloured if repliated in a given tissue (otherwise they are light grey).
Colours used to denote each tissue type :-
- brain - Brain
- RPE - Retinal Pigmented Epithelium (eye)
- palate - Palate
- Tongue - Tongue
- ventricle - Ventricle (heart)
- Lung - Lung
- Thyroid - Thyroid (and parathyroid)
- Stomach - Stomach
- pancreas - Pancreas
- liver - Liver
- adrenal - Adrenal gland
- kidney - Kidney
- testes - Testes
- upperlimb - Upper limb
- lowerlimb - Lower limb
Methods
- Embryonic ChIP-seq mapped to hg38 using STAR.
- Uniquely mapped reads counted into 1kb bins using csaw
- Normalisation of read counts through downsampling using subseq with the 99th percentile as sample weight
- 1kb bins were called as marked using sample-specific thresholds. See this script.
- Replicated bins are those called in both samples of a given tissue type
Credits
We are very grateful to all women who consented to take part in our research programme and for the assistance of research nurses and clinical colleagues at Central Manchester University Hospitals NHS Foundation Trust. We thank Ian Donaldson, Peter Briggs and Andy Hayes of the Bioinformatics and Genomic Technologies Core Facilities at the University of Manchester for assistance with RNA-sequencing. REJ is a UK Medical Research Council (MRC) clinical research training fellow. NAH is a Wellcome Trust senior fellow in clinical science (WT088566MA). This project received support from the Wellcome Trust (WT097820) with additional support from MRC project grants MR/L009986/1 to NB and NAH, the British Council (14BX15NHBG) to NAH and MR/J003352/1 to KPH.
References
This data is unpublished. Please do not share without prior permission of neil.hanley@manchester.ac.uk