biostudies-arrayexpressHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14491The aim of this study was to identify miRNAs that undergo regulated biogenesis in response to ionizing radiation in B-lymphoma cells. The dataset includes RNA 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. Paired-end RNA sequencing was performed using the Illumina platform. Chromosomal coordinates of the human miRNAs (GRCh38) were downloaded from miRBase (hsa.gff3, miRBase v22), and the coordinates were extended by 150 bp upstream and downstream to designate pri-miRNA transcripts. This modified file was then merged with the base GTF annotation. The raw data underwent preprocessing to remove adapters and low-quality reads using TrimGalore-0.6.6. The cleaned reads were then aligned to the reference genome using STAR-2.7.3a. Genome sequence (GRCh38.primary_assembly.genome.fa) and primary annotations (gencode.v41.primary_assembly.annotation.gtf) were obtained from the GENCODE database (https://www.gencodegenes.org/human/ ). FeatureCounts from the Subread 2.0.3 package was used for read quantification.biostudies-arrayexpressSample Collection - Burkitt lymphoma and Hodgkin lymphoma cell lines were exposed to ionizing radiation at a dose of 4 Gy and collected 4h and 12h upon irradiation, control unirradiated cells were collected at 4h timepoint.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. Upon isolation, RNA was treated with and RNase-Free DNase Set (Qiagen, Cat. No. 79254), to remove possibly remaining DNA.Library Construction - Libraries were generated with Illumina TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold. Standard fragmentation conditions were used (90°C for 2 minutes to obtain 150 nt sequences (modified from standard 94°C for 4 minutes).Sequencing - Libraries were sequenced on Illumina NovaSeq6000 platform, using the following settings: 2x150 (paired end sequencing with 150nt reads), read depth of coverage: >100M reads/sample.MINSEQE ScoreAssays and DataProcessed DataorganisationMAGE-TAB FilesData Transformation - Genes, to which at least 10 reads were aligned in a single sample, were retained. Read counts were normalized in edgeR using TMM (Trimmed Mean of Mvalues) algorithm and converted to CPM values (Counts Per Million).Sequence Alignment - Adapter sequences and low quality bases (Phred<20) were trimmed using TrimGalore ver. 0.6.7. Trimmed reads shorter than 20nt were removed. Processed reads (on average 130M/sample) were aligned to the GRCh38 reference genome using STAR ver. 2.7.10a [6], with GENCODE gene annotation database ver. 41 (comprehensive, primary regions). The average alignment rate for all samples was 94.4%. Read counts for individual genes were obtained using featureCounts from the Subread package [8], using GENCODE annotation database cobined with miRbase GRCh38 hairpin coordinates, extended by +/-150bp.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensE-MTAB-14492Izabella Ślęzak-ProchazkaWiktoria PłonkaRoman JaksikfalsePri-miRNA 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 RNA 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. Paired-end RNA sequencing was performed using the Illumina platform. Chromosomal coordinates of the human miRNAs (GRCh38) were downloaded from miRBase (hsa.gff3, miRBase v22), and the coordinates were extended by 150 bp upstream and downstream to designate pri-miRNA transcripts. This modified file was then merged with the base GTF annotation. The raw data underwent preprocessing to remove adapters and low-quality reads using TrimGalore-0.6.6. The cleaned reads were then aligned to the reference genome using STAR-2.7.3a. Genome sequence (GRCh38.primary_assembly.genome.fa) and primary annotations (gencode.v41.primary_assembly.annotation.gtf) were obtained from the GENCODE database (https://www.gencodegenes.org/human/ ). FeatureCounts from the Subread 2.0.3 package was used for read quantification.2025-11-30T00:00:00Z2026-05-27T17:44:20.689Z2024-10-01T10:29:09.32ZE-MTAB-14491ERP164657E-MTAB-14492EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184