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Pri-miRNA Expression Profiles in Burkitt and Hodgkin lymphoma cell lines upon Ionizing Radiation Exposure

ABSTRACT: Pri-miRNA Expression Profiles in Burkitt and Hodgkin lymphoma cell lines upon Ionizing Radiation Exposure

PROVIDER: PRJEB80702 | ENA |

REPOSITORIES: ENA

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Pri-miRNA Expression Profiles in Burkitt and Hodgkin lymphoma cell lines upon Ionizing Radiation Exposure

Project description:The 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.

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miRNA Expression Profiles in Burkitt and Hodgkin lymphoma cell lines upon Ionizing Radiation Exposure

Project description:The 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, customized to fit miRge2 specifications. An iterative alignment strategy was employed: the reads were initially mapped to mature miRNA sequences from miRBase v22.1, and those that remained unaligned were subsequently mapped to miRNA hairpin sequences, non-coding RNAs, and the Ensembl cDNA database. Any unaligned reads were re-aligned to mature miRNA sequences under more relaxed conditions.

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miRNA Expression Profiles in Burkitt and Hodgkin lymphoma cell lines upon Ionizing Radiation Exposure

Project description:miRNA Expression Profiles in Burkitt and Hodgkin lymphoma cell lines upon Ionizing Radiation Exposure

| PRJEB80701 | ENA

Expression data from Burkitt lymphoma cases

Project description:Burkitt lymphoma is the commonest cancer in children in Africa. We compared the gene expression profiles of African Burkitt lymphoma patients with those of cases presented in Western countries in both immunocompetent (sporadic Burkitt lymphoma) and HIV-infected patients (immunodeficiency associated Burkitt lymphoma). We used microarrays to detail the global programme of gene expression in different subtypes of Burkitt lymphoma.

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