READ ME File For 'Supplementary Data for Integration of genomic variation, ileal transcriptomics and longitudinal clinical data in paediatric inflammatory bowel disease'

Dataset DOI: https://doi.org/10.5258/SOTON/D1657 

ReadMe Author: Dr James Ashton, University of Southampton orcid.org/0000-0003-0348-8198

This dataset supports the thesis entitled Integration of genomic variation, ileal transcriptomics and longitudinal clinical data in paediatric inflammatory bowel disease
AWARDED BY: University of Southampton
DATE OF AWARD: 2020

DESCRIPTION OF THE DATA
These data contain additional datasets (including genomic, transcriptomic and microbiome data), standard operating procedures (including biological sampling, processing and storage) and study paperwork (including PIS, protocol, consent forms and ethical documentation) related the above thesis. These data are intended to support the reading of this thesis. 

This dataset contains:

•	Microbiome
o	Quality control
o	Taxonomy
o	Phylogenetic trees
•	Chapter 3
o	All blood results
•	Chapter 4
o	Data available for all patients
o	Segregation analysis 
o	Monogenic genes in analysis 
o	Functional evidence table 
o	Correct zygosity variants
o	NOD2 variants
o	Compound heterozygous variants
o	Ileal disease correction analysis
o	Surgical resection analysis 
•	Chapter 5
o	Raw data NADPH oxidase complex genes CADD 1.6
o	Regression analysis 
•	Chapter 6
o	RNA extraction quality control 
o	Genes in WGCNA modules 
o	Module 3 pathways 
o	DEGs controls vs patients
o	DEGs ED patients vs controls
o	WGCNA gene module membership 
o	Blue module enrichment analysis 
•	Chapter 7
o	Autoimmune gene list- LOEUF correction
o	Annotated NOD pathway VCF
o	Genomic and RNA integration raw data
o	Module hub genes variation 
Standard operating procedures 
Collection of samples-
1.	Biopsy samples
2.	Blood collection
3.	Faecal collection
4.	Plasma collection
Storage of samples 
1.	Biopsy storage 
2.	Faecal sample storage 
Processing-
1.	Biopsy processing
a.	Bacterial DNA
b.	Human RNA
2.	DNA
a.	From blood
b.	From saliva 
3.	Plasma
a.	From whole blood 
4.	Faecal samples
a.	Bacterial DNA
b.	Faecal calprotectin
Genetics of PIBD study paperwork 
1.	Consent forms
2.	Letters for results 
3.	Patient information sheets
4.	Data collection proformas
5.	Study protocol 


Date of data collection: 01/09/2017-01/09/2020

Licence:
CC BY

Related projects/Funders:
Funded by Action Medical Research


Date that the file was created: November 2020