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Series GSE106458 Query DataSets for GSE106458
Status Public on Dec 16, 2017
Title Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq
Organism Mus musculus
Experiment type Other
Summary For high-throughput sequencing and quantification of immunoglobulin repertoires, most methodologies utilise RNA. However, output varies enormously between recombined genes due to different promoter strengths and differential activation of lymphocyte subsets, precluding quantitation of recombinants on a per cell basis. To date, DNA-based approaches have used V gene primer cocktails, with substantial inherent biases. Here we describe VDJ-seq, which accurately quantitates immunoglobulin diversity at the DNA level in an unbiased manner. This is accomplished with a single primer extension step using biotinylated J gene primers. By addition of unique molecular identifiers (UMI) before primer extension, we reliably remove duplicate sequences and correct for sequencing and PCR errors. Furthermore, VDJ-seq captures productive and non-productive VDJ and DJ recombination events on a per cell basis. Library preparation takes 3 days, with 2 days of sequencing, and 1 day of data processing and analysis.
Overall design A range of starting material concentrations 500ng-5µg and examining different combination of DNA polymerases
Contributor(s) Chovanec P, Corcoran A
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Submission date Nov 02, 2017
Last update date May 15, 2019
Contact name Felix Krueger
Organization name Altos Labs
Department Bioinformatics
Street address Granta Park
City Cambridge
ZIP/Postal code CB21 6GP
Country United Kingdom
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (6)
GSM2837806 1ug
GSM2837807 2_5ug
GSM2837808 500ng
BioProject PRJNA416923
SRA SRP123508

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Supplementary file Size Download File type/resource
GSE106458_RAW.tar 40.5 Mb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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