biostudies-arrayexpressHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14492The aim of this study was to identify miRNAs that undergo regulated biogenesis in response to ionizing radiation in B-lymphoma cells. The dataset includes miRNA sequencing data from three Burkitt lymphoma cell lines (ST486, CA46, DG75) and three Hodgkin lymphoma cell lines (L1236, L428, KMH2). Cells were exposed to 4 Gy dose of ionizing radiation and compared to non-irradiated control cells. Single-end RNA sequencing was performed using the Illumina NextSeq500, platform, generating high-quality reads for the analysis of miRNA expression levels and gene expression profiles related to miRNA biogenesis. The raw data analysis followed a multi-step approach. Adapter sequences were removed with Cutadapt-1.11. The reads were then aligned to a modified miRBase (v22.1) using Bowtie-1.2.2, customizebiostudies-arrayexpressSample Collection - Burkitt lymphoma and Hodgkin lymphoma cell lines were exposed to ionizing radiation at a dose of 4 Gy and collected 1h, 4h and 12h upon irradiation, control unirradiated cells were collected at 4h timepoint.Sequencing - Libraries were sequenced on Illumina NextSeq500 platform, using the following settings: 1x75 (single-end sequencing with 75bp reads), read depth of 12 -14 million reads on average.Nucleic Acid Extraction - Total RNA was extracted using the miRNeasy Mini Kit (QIAGEN, Cat. No. 1038703). This kit is specifically designed for the isolation of high-quality RNA, including small RNAs such as miRNA, from a variety of sample types. After addition of chloroform, Heavy 5PRIME Phase Lock GelTM (QuantaBio, Cat. No. 2302830) was applied to improve organic/inorganic phase separation.Library Construction - Quality control of RNA was performed using Bioanalyzer. A gel-free, bead-based size selection procedure was applied to isolate RNA fragments ranging between 15 and 40 nucleotides. Libraries were generated with Illumina QIAseq miRNA Library Kit and integrated UMI technology was applied.MINSEQE ScoreAssays and DataProcessed DataorganisationMAGE-TAB FilesData Transformation - Both known and candidate novel miRNAs, to which at least 10 reads were aligned in a single sample, were selected for further study. Read counts were normalized in edgeR using TMM (Trimmed Mean of Mvalues) algorithm and converted to CPM values (Counts Per Million).Sequence Alignment - Raw sequencing reads were processed using miRge2, which included adapter-trimming based on Cutadapt and aligned based on Bowtie. The alignment was conducted in multiple stages where first reads were aligned to mature miRNA sequences (miRBase22.1); unaligned reads were sequentially matched against hairpin miRNA (miRBase22.1), noncoding RNAs, Ensembl cDNA database, and again to mature miRNA sequences (miRBase22.1), using less stringent criteria. Detection of candidate novel miRNAs was based on miRge2 for each individual sample. The results were later combined between samples based on genomic coordinates of identified miRNAs (partial overlap was considered sufficient).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500microRNA profiling by high throughput sequencingHomo sapiensE-MTAB-14491Izabella Ślęzak-ProchazkaWiktoria PłonkaRoman JaksikfalsemiRNA Expression Profiles in Burkitt and Hodgkin lymphoma cell lines upon Ionizing Radiation ExposureThe aim of this study was to identify miRNAs that undergo regulated biogenesis in response to ionizing radiation in B-lymphoma cells. The dataset includes miRNA sequencing data from three Burkitt lymphoma cell lines (ST486, CA46, DG75) and three Hodgkin lymphoma cell lines (L1236, L428, KMH2). Cells were exposed to 4 Gy dose of ionizing radiation and compared to non-irradiated control cells. Single-end RNA sequencing was performed using the Illumina NextSeq500, platform, generating high-quality reads for the analysis of miRNA expression levels and gene expression profiles related to miRNA biogenesis. The raw data analysis followed a multi-step approach. Adapter sequences were removed with Cutadapt-1.11. The reads were then aligned to a modified miRBase (v22.1) using Bowtie-1.2.2, customize2025-11-30T00:00:00Z2026-06-16T13:40:40.683Z2024-10-01T10:30:33.015ZE-MTAB-14492ERP164656E-MTAB-14491EFO_0002944EFO_0004170EFO_0002896EFO_0004917EFO_0005518EFO_0003816EFO_0004184