Genome-wide identification of distinct miRNA-mRNA target regulation pairs in Non-Hodgkin lymphomas: a report from the ICGC MMML-Seq consortium

Study ID Alternative Stable ID Type
EGAS00001001394 Other

Study Description

We obtained miRNA profiles by miRnome sequencing from ICGC MMML-Seq patients diagnosed with Burkitt lymphoma, diffuse large B-cell lymphoma and follicular lymphoma and provide evidence of subtype-specific miRNA expression differences. We describe differentially expressed, mutated, edited and not previously annotated miRNAs. Addditionally, by performing argonaute-2 photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) experiments, we obtained a set of biochemically-validated miRNA binding sites and identified miRNA-mRNA interaction pairs with a negative correlation in patient RNASeq data.

Study Datasets 6 dataset.

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Dataset ID Description Technology Samples
EGAD00001001468 PAR-CLIP was performed on the Argonaute-2 protein (AGO2) in four lymphoma cell lines:NamalwaRajiSU-DHL-4SU-DHL-6 Illumina HiSeq 2500 4
EGAD00001001612 After overexpression and knockdown of both described novel miRs nmiR-1 and nmiR-2 in BL cell lines (SU-DHL4 for nmiR-1 and Raji for nmiR-2), we performed regular RNA-Seq (including Mock controls for all cell lines) to identify their direct and indirect downstream mRNA targets. Illumina HiSeq 2500 16
EGAD00001001619 miRNA seq data of 43 cases out of dataset EGAD00001000650 (MMML) 43
EGAD00001001632 miRNA seq data of 13 cases (MMML) 13
EGAD00001001672 Part of RNA sequencing data of Malignant Lymphoma Study (ICGC) Illumina HiSeq 2000 56
EGAD00001001673 Part of WGS seq data of Maligant Lymphoma study (ICGC) Illumina HiSeq 2000 Illumina HiSeq 2500 112

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Publications Citations
Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis.
Haematologica 101:2016 1380-1389