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Genetics of gene expression in primary human immune cells Data Access Committee

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julian@well.ox.ac.uk

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This DAC controls 17 datasets

Dataset ID	Description	Technology	Samples
EGAD00001006979	PacBio long-read circular consensus (CCS) sequencing data for individual HV31 generated on PacBio Sequel II instrument, using size-selected (10-15 kb) DNA from CD14+ monocytes, to a sequencing depth of ~12×. Sequencing was performed at the Wellcome Sanger Institute.	Sequel	1
EGAD00001007020	This submission is of the sequencing data used in the CRISPR iPSC methods paper. Specifically it is 3 fastq files that each represent a replicate of an experiment to transduce the Toronto KnockOut CRISPR Library - Version 3 (TKOv3) into inferred pluripotent stem cell (iPSC) derived macrophages. The sequencing is of the guide RNAs from the TKOv3 having been extracted from the transduced iPSC derived macrophages.		3
EGAD00001007042	Illumina PCR-free sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~44×. Sequencing was performed at the Wellcome Centre for Human Genetics on the Illumina Novaseq platform.	unspecified	1
EGAD00001007043	Oxford Nanopore long-read sequencing data for individual HV31 generated using DNA from CD14+ monocytes, to a sequencing depth of ~63×. Sequencing was performed at the Wellcome Centre for Human Genetics using the Oxford Nanopore PromethION platform.	PromethION	1
EGAD00001007044	MGI standard short-read sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~57×.	unspecified	1
EGAD00001007045	MGI single-tube long fragment read (stLFR) linked-read sequencing data for individual HV31 generated using DNA from CD14+ monocytes, to a sequencing depth of ~51×.	unspecified	1
EGAD00001007046	10x linked-read sequencing data for individual HV31 generated using DNA from CD14+ monocytes, to a sequencing depth of ~40×. Sequencing was performed at Bart’s and the London Genome Centre on the Illumina HiSeq platform.	unspecified	1
EGAD00001007047	PacBio continuous long read (CLR) sequencing data for individual HV31 generated on PacBio Sequel II instrument, using DNA from CD14+ monocytes, to a sequencing depth of ~35×. Sequencing was performed at the Wellcome Sanger Institute.	Sequel	1
EGAD00001007048	MGI CoolMPS short-read sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~57×.	unspecified	1
EGAD00001007049	Bionano DLS optical mapping data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a molecule depth of ~153×. Optical mapping was performed at the Weatherall Institute of Molecular Medicine using the Bionano Saphyr platform.		1
EGAD00001007050	De novo assembly of eight immune system regions for individual HV31, generated using a multi-platform pipeline. A full description of the generation of these assemblies can be found at https://doi.org/10.1101/2021.02.03.429586.		1
EGAD00001007761	This file contains read identifiers for local CCS, CLR, ONT and MGI reads for each of the eight selected genomic regions (HLA, KIR, IGH, IGK, IGL, TRA, TRD, andTRG). We extracted these reads by aligning whole-genome sequencing data to a draft whole-genome de novo assembly, and selecting reads that map to contigs representing each region. These reads were involved in the polishing and validation of the HV31 assembly. Please refer to the relevant manuscript (https://doi.org/10.1101/2021.02.03.429586) for additional details. Read identifiers are stored in JSON format. Along with the full FASTQ files, this file enables convenient re-analysis of the HV31 sequencing data in the eight selected regions.		1
EGAD00001008758	This dataset consists of functional genomic data from 20 Ankylosing Spondylitis patients and 35 Healthy Controls taken from CD4+ T cells, CD8+ T cells and CD14 Monocytes. It contains 364 paired end fastq files consisting of 104 total RNA-seq samples and 116 ATAC samples, for ChIP there are 46 H3K4me3 samples, 46 H3K27ac samples and 3 H3K4me1 samples, along with 49 paired input samples. The samples were sequenced on Illumina HiSeq4000, Illumina NextSeq500 and Illumina NovaSeq 6000 platforms.	Illumina HiSeq 4000 Illumina NovaSeq 6000 NextSeq 500	364
EGAD00010000144	Healthy volunteer collection of European Ancestry	Illumin OmniExpress v1.0 - Illumina GenomeStudio	288
EGAD00010000520	Healthy volunteer collection of European Ancestry	Illumina OmniExpress v1.0-Illumina GenomeStudio	144
EGAD00010002475	HC genotyping data for lead SNPs using Illuminia Global Array V2.0		1
EGAD00010002476	AS genotyping data for lead SNPs using Illuminia Global Array V2.0	Illuminia Global Array V2.0	40