Study

Using de novo assembly to identify structural variation of complex immune system gene regions

Study ID Alternative Stable ID Type
EGAS00001005046 Other

Study Description

Driven by the necessity to survive environmental pathogens, the human immune system has evolved exceptional diversity and plasticity. Several factors contribute to this including inheritable structural polymorphism of the underlying genes. To investigate this we generated data for a single healthy European individual (identified as HV31) using multiple long-read (PacBio Sequel II and Oxford Nanopore), short-read (Illumina HiSeq and MGI G400) and linked-read (10X Chromium and stLFR) sequencing platforms, and optical mapping using the Bionano Saphyr platform. DNA was extracted from monocytes or from peripheral blood mononuclear cells. We used these data to assemble a set of regions encoding components of the immune system and to investigate structural variation. The raw data and analysis results are deposited here for generate research use. A complete description of these data and results can be found in the accompanying article at https://doi.org/10.1101/2021.02.03.429586.

Study Datasets 10 datasets.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

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
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

Who archives the data?

There are no publications available