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 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.

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 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. 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) miRNA seq data of 43 cases out of dataset EGAD00001000650 (MMML)		43
EGAD00001001632	miRNA seq data of 13 cases (MMML) miRNA seq data of 13 cases (MMML)		13
EGAD00001001672	Part of RNA sequencing data of Malignant Lymphoma Study (ICGC) 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) Part of WGS seq data of Maligant Lymphoma study (ICGC)	Illumina HiSeq 2000,Illumina HiSeq 2500	112

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

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

EGAD00001001619

miRNA seq data of 43 cases out of dataset EGAD00001000650 (MMML)

EGAD00001001632

miRNA seq data of 13 cases (MMML)

EGAD00001001672

Part of RNA sequencing data of Malignant Lymphoma Study (ICGC)

Illumina HiSeq 2000

EGAD00001001673

Part of WGS seq data of Maligant Lymphoma study (ICGC)

Illumina HiSeq 2000,Illumina HiSeq 2500

112