{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Gal Dadi"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17140"],"description":["This is a deep targeted sequencing of human peripheral blood B cells and Germline control for lymphoma recurrently mutated genes using custom targeted panel using MIPs in duplicates"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Peripheral blood (PB) was collected from healthy donors, patients with autoimmune disease, and patients with diffuse large B-cell lymphoma (DLBCL) following written informed consent and institutional review board approval. Blood was drawn into EDTA anticoagulant tubes and processed within 4 hours of collection. Peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Paque density gradient centrifugation according to the manufacturer’s instructions. PBMCs were washed twice in PBS and either processed immediately for cell enrichment and flow cytometric sorting or cryopreserved in fetal bovine serum supplemented with 10% DMSO and stored in liquid nitrogen until further use.","Sequencing - Libraries were sequenced on Illumina NovaSeq 6000 or NovaSeq X instruments using 2 × 150 bp paired-end reads. Approximately 20 million paired-end reads were generated per technical replicate library for targeted mutation profiling. Base calling and demultiplexing were performed using Illumina standard pipelines. Sequencing quality was assessed using standard quality control metrics prior to downstream analysis.","Nucleic Acid Extraction - Genomic DNA was extracted from sorted Aged B cells, Memory B cells, and CD19⁻ fractions using the QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s protocol. DNA from diagnostic tumor biopsies (formalin-fixed paraffin-embedded tissue) was extracted using the MagMAX™ FFPE DNA/RNA Ultra Kit (Thermo Fisher Scientific). DNA concentration was measured using Qubit fluorometry, and samples were normalized to ~50 ng input per library preparation when possible. When DNA yield was limiting, samples were concentrated using DNA Clean & Concentrator columns (Zymo Research).","Library Construction - Targeted DNA libraries were prepared using a custom molecular inversion probe (MIP) panel targeting 91 genes recurrently mutated in diffuse large B-cell lymphoma. Libraries were generated according to the manufacturer’s protocol (Sequentify Ltd.) with unique molecular identifiers (UMIs) incorporated to enable molecular deduplication and error correction. For each sample, two independent technical replicate libraries were generated from the same genomic DNA input. Libraries were amplified by PCR, purified using AMPure XP beads, and quantified prior to sequencing. For immunoglobulin heavy-chain (IGH) repertoire analysis, targeted amplification of V(D)J junctions was performed using a dedicated IGH sequencing assay according to the manufacturer’s protocol."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Sequencing reads were processed using a standardized alignment and post-processing pipeline. Briefly, raw sequencing reads were aligned to the human reference genome (GRCh38) using BWA-MEM. Resulting BAM files were sorted and indexed. Read groups were added and BAM files were realigned around indels where applicable. PCR duplicates were marked and removed. Base quality score recalibration was applied when appropriate. No expression-level normalization or count-based transformation was performed at this stage, as the submitted files represent processed alignment files (BAM) intended for downstream variant calling. All downstream analyses (error-corrected variant calling and IGH repertoire profiling) were performed using custom pipelines as described in the associated manuscript."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["DNA-seq"],"species":["Homo sapiens"],"pubmed_authors":["Gal Dadi"],"additional_accession":[]},"is_claimable":false,"name":"DNA sequencing of lymphoma related genes in human mononuclear cells","description":"This is a deep targeted sequencing of human peripheral blood B cells and Germline control for lymphoma recurrently mutated genes using custom targeted panel using MIPs in duplicates","dates":{"release":"2026-06-27T00:00:00Z","modification":"2026-06-27T01:00:41.987Z","creation":"2026-06-10T15:31:24.236Z"},"accession":"E-MTAB-17140","cross_references":{"ENA":["ERP194842"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184"]}}