Copied to clipboard!

scRNA-seq of CD45+ lymphocytes from 22q11.2del patients

Patients with inborn error of immunity (IEI), particularly those affecting T-cell development, provide a unique opportunity to analyse the shape of the human cILC compartment. Frozen samples of four 22q11.2del patients (P20-P23, table 1) were stained with anti-human CD45-APC/Cy7 antibody after thawing and each patient sample was sorted on CD45+ lymphocytes. Freshly sorted CD45+ lymphocytes of each patient were multiplexed per donor and multiple tags were used per donor, depending on cell counts. In total, 10 different oligo-coupled sample tag antibodies were used. To increase the yield, patients with higher cell counts were tagged with multiple tags (3x tags P20 and P22, 2x tags for P21, and 1x tag for P23) and combined with Abseq staining. Next, scRNA-seq was performed from four 22q11.2del patients using the BD Rhapsody pipeline. Total cILC counts were reduced, primarily driven by a marked reduction of cILC1s. scRNAseq analyses showed that cILC1s shared T-cell-associated gene programs.

Type: Transcriptome Sequencing
Archive: European Genome-phenome Archive (EGA)

1 Dataset

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
EGAD50000002769	scRNA-seq was performed on the BD Rhapsody platform. CD45+ lymphocytes four patients P20-23 carrying heterozygous 22q11.2del mutations were sorted from frozen cryopreserved samples. The samples were split and each sample was stained with Sampletag antibodies before Abseq staining with the BD Immune Discovery panel and 6 additional antibodies was performed to better classify immune cell subsets. The sorted and stained populations were pooled before loading onto the BD Rhapsody cartridge. The manufacturer's protocol was followed for library construction and samples were sequenced on an Illumina NovaSeq 6000.	Illumina NovaSeq 6000	1