LUMC Department Pediatrics, Laboratory for Pediatric Immunology

Sequencing Analysis Support Core
sasc@lumc.nl

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Dataset ID	Description	Technology	Samples
EGAD50000002072	The dataset contains five samples from P1, one pre-HSCT and four post-HSCT, one sample from P2 and 5-6 HD. RNAseq reads were processed using the LUMC BIOWDL RNAseq pipeline v5.0.0 (https://github.com/biowdl/RNA-seq). Genes with log2CPM≥1 in at least 10% of all samples were retained for downstream analysis. Differential gene expression analysis was performed using the dgeAnalysis R-Shiny application (https://github.com/LUMC/dgeAnalysis/tree/v1.4.4). ATACseq reads were processed using the LUMC BIOWDL Chipseq pipeline 1.0.0-dev (https://github.com/biowdl/ChIP-seq).	Illumina NovaSeq 6000	12
EGAD50000002970	This dataset contains immunoglobulin heavy-chain (IGH) B-cell receptor repertoire sequencing data generated from peripheral blood samples of 10 pediatric recipients of allogeneic hematopoietic stem cell transplantation and 10 age-matched healthy donors. Patient samples were collected longitudinally during routine post-transplant follow-up, enabling assessment of BCR repertoire reconstitution over time. PBMC-derived total RNA was reverse transcribed to full-length cDNA, followed by multiplex PCR amplification of IGH transcripts covering IGHM, IGHG and IGHA. Libraries were prepared using the KAPA HyperPrep Kit and sequenced as paired-end reads on an Illumina MiSeq using the MiSeq Reagent Kit v3.	Illumina MiSeq	150